Stokes was deemed fit enough to play a big part in sealing a series win for England in Saturday's latest meeting, though, hitting a century in the second one-day global despite being in obvious discomfort at times.
Coming to the South African team, they could not cross the finishing line in the second ODI despite some heroics with the bat displayed by David Miller and Chris Morris.
Ben Stokes cashed in on his remarkable early fortune as his century helped England set South Africa 330 for six in the second Royal London Series match at the Ageas Bowl.
Stokes hit a century in the second ODI win against South Africa on Saturday, but the knee injury that troubled him in the first ODI meant he could only bowl three overs.
England allrounder Ben Stokes has conceded his troublesome knee is affecting his bowling following his match-winning hundred against South Africa in Southampton.
Just over two years since a defeat by Bangladesh in Adelaide sealed their embarrassing first-round exit from the 2015 World Cup, England face the Tigers in the Champions Trophy opener at The Oval on Thursday, with genuine optimism that they can at last win a first major one-day global tournament.
There are no such physical issues troubling South Africa as yet, but captain AB de Villiers knows a win on the board would be decidedly handy before the impending global tournament.
Root (39) looked to be heading for a big score until an Eoin Morgan drive clipped Pretorius' finger before clattering into the stumps at the non-strikers end with the England star short of his ground. The 46th over, bowled by Andile Phehlukwayo, went for 22 as 111 flowed from the last ten; only Rabada, who picked up 2 for 50, managed to go at less than a run a ball for South Africa.
Kyle Busch turns fastest lap at Pocono for 2nd straight pole
Busch poked fun at his terse response-and-drop to a question a couple of weeks ago that was scrutinized around NASCAR. The Joe Gibbs Racing star really went through the paces in this final chance to dial-in for Sunday's race.
Yet it is the injury to Stokes which is giving cause for concern given his importance with both bat and ball.
Maharaj endured three off the dropped catches off his bowling, Stokes badly put down first by Hashim Amla at slip and then by De Kock.
Stokes finally fell in the 44th over when he holed out in the deep to give debutante left-arm spinner Keshav Maharaj (1-72) his lone wicket.
The innings then took a decisive turn when Stokes was missed twice in his first two balls, with Maharaj again the unfortunate bowler.
Morgan and Stokes wrought the advantage for England with a stand of 95 that was ended in the 33rd over when Rabada dismissed Morgan for 45 with De Kock diving forward to snare a low catch.
To rub salt in the wound, Stokes edged the very next ball too but De Kock dropped the chance.
England appeared to be heading for defeat when South Africa required just eight runs off eight balls with five wickets in hand.
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