With 9 wickets still in hand, including Alastair Cook now unbeaten on 59, they hold a very strong hand with the spinners becoming increasingly dominant in the game and the pitch getting lower and slower. He did not take the field for the first 38 overs of the England innings but returned for the final 13, although he did not bowl.
South Africa resumed on 214 for five - still 244 runs behind an England total which featured Joe Root's 190 in his first Test as England captain as well as fifties from Moeen Ali (87), Stuart Broad (57 not out) and Stokes (56).
Philander made an 80-ball fifty before he was last man out slogging at Ali, who finished with impressive figures of four for 59 in 20 overs.
The tall fast bowler then doubled up with the wicket of Liam Dawson, lbw for a second-ball duck in his second Test, before Moeen and Broad took over.
On the first ball of the day's third over, Root edged behind a delivery from Morne Morkel and looked thoroughly miserable as he walked off to a standing ovation, having missed the chance to register a second double century at Lord's after one against Sri Lanka in 2014.
Broad's crowd-pleasing turn was a 45-ball 50 which he completed with successive pulled sixes off Morkel to add to his seven fours as he and James Anderson compounded South Africa's frustrations in an entertaining 10th-wicket stand of 45 from just 27 deliveries.
South Africa found themselves 104-4 at one point but a century partnership between Temba Bavuma and Theunis de Bruyn saw the tourists past 200 at the close.
Mattek-Sands thanks fans for messages after her horror injury
But she questioned why it took the medical services so long to react to her friend's distress. 'Please help me, please, please . Speaking of the gravity of the injury Cirstea said, "I think the kneecap, it was out".
Good morning and welcome to live coverage of day three of the first Test between England and South Africa.
South Africa ended day two on 214/5 and will continue batting on Saturday at 11:00 local time or 10:00 GMT.
South Africa trailed by 362 runs and was only going along at three an over.
Ali's twirl then undid Bavuma - who had brought up his seventh Test fifty from 114 balls with a square drive off Stokes - in the following over, Stokes pouching the ball at slip after it had deflected off Bairstow's thigh.
The 32-year-old could have been stumped on 31 early in the evening session, too, but De Kock could not gather the ball cleanly when part-time spinner JP Duminy pushed the ball down the leg side.
Having batted for most of the first day, Root did not last long second time around, drawn into pushing at a delivery of ideal length from Morkel, which seamed a fraction to take the outside edge.