Starting the day on 153 for three, Pakistan lost their remaining seven wickets for 120 runs to be bowled out for 273.
Philander struck twice in the first over of the day. He had Shaun Marsh caught at gully off the first ball. An inside edge looped off the batsman's thigh pad to Temba Bavuma.
Rabada was found guilty of "inappropriate and deliberate physical contact with a player" after leaning with his shoulder into Steve Smith after dismissing the Australian skipper last week.
South African pacer Vernon Philander said that they would not lower their guard in the final Test as they are eyeing a whitewash against a beleaguered Indian side.
While Dale Steyn has been ruled out of the remaining matches with a heel injury, the Proteas on Tuesday added rookie pacers Duanne Olivier, Lungi Ngidi to their attack.
Vernon Philander returned with career-best figures of 6/42 as South Africa cantered to a 72-run win.
The bowlers had given India big hopes after bowling out South Africa for 130 in their second innings, setting a target of 208 to win the match
Vernon Philander led a truncated South African bowling attack with a fine display as he, along with Morne Morkel and Kagiso Rabada, helped the Proteas dismiss India for 135 to give the host a 72-run win and a 1-0 lead in the three-Test series.
India all-rounder Hardik Pandya stood tall amid ruins with his all-round prowess but could not prevent South Africa from finishing on top on Day 2 of the first Test at Newlands Cricket Ground in Cape Town on Saturday.
India were in deep trouble at 28 for 3 after bowlers dismissed South Africa for a modest 286 on the opening day of the first Test.
Vernon Philander questioned India's claims of being fully prepared for the three-match series, saying a fair assessment of where the visitors stand could only be made after the first Test beginning Friday.
England were 171 for four at stumps, having won the toss, with 31 of the scheduled 90 overs lost to bad weather on the opening day of the 100th Test at The Oval.
England, set a mammoth 474 runs for victory, collapsed to 133 all out in their second innings 40 minutes before tea on the fourth day.
South Africa's unbeaten half-century revived the visitors after Stuart Broad sparked a collapse.
How to watch Day 4 of England vs South Africa 1st Test match. Read all about live coverage and Test match action from the Lord's in London on July 9, 2017.
England were 119 for one in their second innings at stumps on the third day, a lead of 216 runs in this opening match of a four-Test series.
Sri Lanka trail South Africa by 346 runs at the close of play on Day 2 of the third and final Test being played at the Wanderers.
Opening batsman Dean Elgar hit a half-century to add to his first innings hundred before South Africa declared their second innings on 224 for seven 45 minutes before tea against Sri Lanka