Australia did get the wicket of Aiden Markram, who was fresh from his magnificient century in the second innings of the first Test.
Naturally it was de Villiers who led the counterattack, taking 14 runs off the next over from Cummins.
Amla scored 56 from 148 balls in a third-wicket partnership of 88 with Dean Elgar (57 from 197 balls) as South Africa reached 263-7 at the close to earn a first innings lead of 20.
Australia otherwise battled to create opportunities to take wickets, not helped by South Africa going into their shell and playing risk-free cricket, though spinner Nathan Lyon did find good turn off the wicket and was hard to score off.
However, the action was overshadowed by events away from the pitch, including Cricket South Africa issuing an apology to Cricket Australia after an incident involving two of their employees being photographed with fans wearing Sonny Bill Williams masks in an apparent attempt to embarrass David Warner.
The hosts dominated the opening two sessions of the day, even if the going was slow at times.
Only 43 runs were scored in 26 overs between lunch and tea after a slightly less pedestrian morning during which 71 runs were scored in 28 overs.
Nightwatchman Kagiso Rabada (29) was the only batsman out in the first two sessions.
A gastro virus continues to play havoc with the second Test in Port Elizabeth after one of the umpires replaced Mitchell Marsh in the sick bay.
Mitchell Starc removes Hashim Amla's off stump with a pinpoint yorker shortly after tea.
One of the elements that livened up a slow day out in the middle, the brass band that has been a popular fixture at St George's Park for two decades, was asked to stop playing by umpires Kumar Dharmasena and Sundaram Ravi. Each ball was just a fraction fuller and straighter until Elgar had no choice but to play, and could only edge through to the keeper as the final delivery left him. Marsh trapped South Africa captain Faf du Plessis and Theunis de Bruyn lbw in successive overs.
The DRS showed the ball was hitting Amla's pad fractionally outside the line and the out of form batsman received an unexpected second chance.
Offspinner Nathan Lyon also made his presence felt with the wicket of de Kock for 9. But with Philander holding his own, de Villiers picked off the bad deliveries and edged South Africa into the lead.