Jennings was 34 not out and Tom Westley, one of three debutants in England's XI, unbeaten on 28 in what is the 100th Test at The Oval.
In his absence the Proteas eventually bowled the hosts out for 353 on day two, Ben Stokes proving a thorn in their side with a crucial 112.
The left-hander saw an edge off Philander fly past Dean Elgar at third slip when he had six to his name and was later adjudged lbw to Kagiso Rabada for 33, only for the decision to be overturned on review due to the ball pitching outside leg stump. Toby Roland-Jones then stole the show with ball with a four-wicket haul and ran through the South African batting line-up and had it in tatters.
South Africa were bolstered by the knowledge that all-rounder Philander had been passed fit after a night on a hospital drip followed a second day's play from which the paceman was largely absent.
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He had just one minor scare on 40, when Ben Stokes nearly pulled off the most brilliant of catches at gully, flinging himself to his left to intercept a skewed drive off Stuart Broad - with the total on 148.
Temba Buvma and Morne Morkel are at the crease and will have this task at their hand.
Stokes could not quite cling on, and in Broad's next over South Africa were safely within 200 runs of England's total after a Bavuma cover-drive for four.
The worth of his more than three-hour innings was acknowledged by South Africa captain Faf du Plessis, who led the applause from the dressing room balcony.
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