Stokes' quickfire brace severely dented South Africa's already slim chances of victory.
Toby Roland-Jones seals maiden five-fer before Keaton Jennings rides his luck to help hosts reach 74-1.
South Africa collapse, with Roland-Jones taking four wickets on debut.
Four-match series now level at 1-1 after hosts suffer another dismal batting collapse.
Hosts need a record fourth-innings run chase of 474 to win match after toiling again on day three.
Proteas boast a lead of 205 after 15 wickets fall on breathless day two at Trent Bridge.
Proteas reach stumps on day one of the second Test on 309-6 as duo dig in to frustrate hosts.
England currently lead the series 1-0 after winning the first Test by 211 runs.
The Lord's encounter will be the first of four Test matches in the series.
South Africa's Imran Tahir dropped down two places in the bowling rankings to third.
The debutant hit 78 before the hosts closed out a 19-run victory.
The series is currently tied at 1-1.
England lead the series 1-0 after their 9-wicket win in the first game.
Duo combine for 98 as hosts easily chase down 143 with 33 balls to spare at the Ageas Bowl.
Virat Kohli has been in fine form in the Champions Trophy so far.
Defending champions set to face Bangladesh at Edgbaston after eight-wicket win at The Oval.
England had clinched the series, but collapsed heavily in the third ODI to lose by 7 wickets.
England have already clinched the series after going 2-0 up against South Africa.
The former Australia cricketer believes four teams have a real shot at winning the tournament.
Proteas fall agonisingly short of winning total thanks to impressive death bowling from Durham paceman.
Chris Woakes marks his return from IPL duty with four wickets in 72-run victory at Headingley.
Security is also getting tightened ahead of England's ODI series against South Africa today (24 May).