But after all that, it came down to the final ball.
Stunning stuff from Mark Wood, gutting for South Africa...
Post update
Provided he's not in danger of missing the Champions Trophy opener against Bangladesh on Thursday, England will be relieved Stokes was able to star in this match.
And there was more encouragement for England's Champions Trophy bid in the shape of Jos Buttler's timely return to form.
The keeper finished unbeaten on 65 from 53 balls, pulling off some typical unorthodox, improvised brilliance.
Post update
There was to be pain later on for Stokes, as he bowled only three overs, his knee that had made him a doubt for this match giving him discomfort.
The all-rounder told the BBC that he's due to have another scan on the knee injury.
Post update
The talismanic all-rounder then reached his century off just 77 balls...
Only to fall after one more run, equalling his highest ODI score of 101.
Post update
South Africa dropped six catches in total, Amla shelling two of them, but his first miss quickly looked the costliest as Stokes started clearing the ropes...
Post update
So earlier on, England passed 300 yet again in one-day internationals, with Ben Stokes hitting his second ODI hundred.
But the all-rounder was dropped on zero by Hashim Amla.
Well, I say drop but in truth the South Africa opener didn't even lay a hand on it...
Bowling affected by knee problem - Stokes
Man of the match Ben Stokes, who made a century for England: "Mark Wood bowled really well and it was an amazing effort from him.
"It shows what a bit of pace does - it makes it harder for batsmen at the end to strike the ball cleanly.
"Batting is fine but my bowling is affected by my knee. I'm not quite sure what it is but I have a couple more scans to come and hopefully it will settle down.
"It's nice to have a bit of form and to hit the ball so cleanly."
Get Involved
#bbccricket
Rex FeaturesCopyright: Rex Features
Seb Constable: Mark Wood, give that man a cookie. That was sensational bowling in the last over!
Mike: English ODI cricket come on so much last few yrs - more batting depth, tactical nous & bowling @ death unrecognisable from before.
Nick Hughes: Sensational bowling Mark Wood! Shamefully nearly switched off when Ball went for 10 at the start of the 19th.
'Woody was awesome' - Morgan
England captain Eoin Morgan: "Those are the sort of games you really want to win, you learn a more from these games.
"It really got away from us for a while but Mark Wood coming up with the goods at the end was awesome.
"The Champions Trophy is bound to be tight so this preparation is ideal and full credit to the Ageas Bowl, with a full house today, it helps us massively for the tournament.
"Woody usually bowls yorkers but he adjusted to the conditions at the end with the short ball and it was really impressive.
"Given the conditions we batted under early on it was difficult to get going but we did fantastic after that. It was a great century from Ben Stokes and good to see Jos Buttler getting runs before the Champions Trophy."
South Africa captain AB de Villiers: "I thought the boys played exceptionally well but England got their plans right and showed guts at the finish.
"The result is unfortunate but I'm proud of the way we played. I thought we paced it really well but we couldn't cross the line.
"I think our fielding was costly. We were a little bit careless at times, conceding one or two more boundaries than we should have done.
"Hopefully we can get a win in the final match to take into the Champions Trophy."
Post update
But Mark Wood has the last word, with a superb final over, conceding just four runs to secure a thrilling two-run victory for England...
Post update
The removal of Behardien just brings Chris Morris to the crease though and his power hitting off length deliveries seems to be leading South Africa towards victory...
Post update
David Miller takes charge with a monstrous six off Moeen Ali, but partner Farhaan Behardien's scratchy innings is finally brought to an end by Plunkett...
Post update
Suddenly Plunkett fires in a brilliant bouncer to remove De Villiers
And then De Kock is gone, just two short of a century...
Post update
But De Kock and AB de Villiers look to be in imperious form...
Post update
Liam Plunkett gets in on the act to remove Faf du Plessis...
Post update
Ben Stokes fails to take a sharp chance off Quinton de Kock but snares fellow opener Hashim Amla soon after...
Post update
So here's the tale of that South Africa innings and thrilling finish, in highlight form...
Live Reporting
Jack Skelton
All times stated are UK
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Latest PostPost update
And that's that for this live text.
The third and final match of the series is at Lord's on Monday.
We'll hopefully see you back here then.
For now, Stephan Shemilt's report of a remarkable match is here.
Farewell!
Post update
But after all that, it came down to the final ball.
Stunning stuff from Mark Wood, gutting for South Africa...
Post update
Provided he's not in danger of missing the Champions Trophy opener against Bangladesh on Thursday, England will be relieved Stokes was able to star in this match.
And there was more encouragement for England's Champions Trophy bid in the shape of Jos Buttler's timely return to form.
The keeper finished unbeaten on 65 from 53 balls, pulling off some typical unorthodox, improvised brilliance.
Post update
There was to be pain later on for Stokes, as he bowled only three overs, his knee that had made him a doubt for this match giving him discomfort.
The all-rounder told the BBC that he's due to have another scan on the knee injury.
Post update
The talismanic all-rounder then reached his century off just 77 balls...
Only to fall after one more run, equalling his highest ODI score of 101.
Post update
South Africa dropped six catches in total, Amla shelling two of them, but his first miss quickly looked the costliest as Stokes started clearing the ropes...
Post update
So earlier on, England passed 300 yet again in one-day internationals, with Ben Stokes hitting his second ODI hundred.
But the all-rounder was dropped on zero by Hashim Amla.
Well, I say drop but in truth the South Africa opener didn't even lay a hand on it...
Bowling affected by knee problem - Stokes
Man of the match Ben Stokes, who made a century for England: "Mark Wood bowled really well and it was an amazing effort from him.
"It shows what a bit of pace does - it makes it harder for batsmen at the end to strike the ball cleanly.
"Batting is fine but my bowling is affected by my knee. I'm not quite sure what it is but I have a couple more scans to come and hopefully it will settle down.
"It's nice to have a bit of form and to hit the ball so cleanly."
Get Involved
#bbccricket
Seb Constable: Mark Wood, give that man a cookie. That was sensational bowling in the last over!
Mike: English ODI cricket come on so much last few yrs - more batting depth, tactical nous & bowling @ death unrecognisable from before.
Nick Hughes: Sensational bowling Mark Wood! Shamefully nearly switched off when Ball went for 10 at the start of the 19th.
'Woody was awesome' - Morgan
England captain Eoin Morgan: "Those are the sort of games you really want to win, you learn a more from these games.
"It really got away from us for a while but Mark Wood coming up with the goods at the end was awesome.
"The Champions Trophy is bound to be tight so this preparation is ideal and full credit to the Ageas Bowl, with a full house today, it helps us massively for the tournament.
"Woody usually bowls yorkers but he adjusted to the conditions at the end with the short ball and it was really impressive.
"Given the conditions we batted under early on it was difficult to get going but we did fantastic after that. It was a great century from Ben Stokes and good to see Jos Buttler getting runs before the Champions Trophy."
Post update
Our fielding was costly - De Villiers
South Africa captain AB de Villiers: "I thought the boys played exceptionally well but England got their plans right and showed guts at the finish.
"The result is unfortunate but I'm proud of the way we played. I thought we paced it really well but we couldn't cross the line.
"I think our fielding was costly. We were a little bit careless at times, conceding one or two more boundaries than we should have done.
"Hopefully we can get a win in the final match to take into the Champions Trophy."
Post update
But Mark Wood has the last word, with a superb final over, conceding just four runs to secure a thrilling two-run victory for England...
Post update
The removal of Behardien just brings Chris Morris to the crease though and his power hitting off length deliveries seems to be leading South Africa towards victory...
Post update
David Miller takes charge with a monstrous six off Moeen Ali, but partner Farhaan Behardien's scratchy innings is finally brought to an end by Plunkett...
Post update
Suddenly Plunkett fires in a brilliant bouncer to remove De Villiers
And then De Kock is gone, just two short of a century...
Post update
But De Kock and AB de Villiers look to be in imperious form...
Post update
Liam Plunkett gets in on the act to remove Faf du Plessis...
Post update
Ben Stokes fails to take a sharp chance off Quinton de Kock but snares fellow opener Hashim Amla soon after...
Post update
So here's the tale of that South Africa innings and thrilling finish, in highlight form...