Philander took six for 42 with Morne Morkel and Kagiso Rabada claiming two wickets each as India were subjected to a pace barrage in bowler-friendly conditions. South Africa were reduced to three fast bowlers because of a heel injury suffered by Dale Steyn while bowling on Saturday.
Earlier, it had been the Indian bowlers who held sway when South Africa were bowled out for 130 in their second innings, losing their last eight wickets for 65 runs. India's run chase started promisingly with Murali Vijay and Shikhar Dhawan putting on 30 for the first wicket, although Vijay was reprieved on review twice after being given out against Philander, for leg before wicket and a catch behind the wicket.
But then Dhawan was caught at gully off his bat handle when he got into a tangle against a lifting ball from Morkel. Six balls later it was third time lucky for Philander as Vijay edged a catch to AB de Villiers at third slip. Philander claimed the key wicket of Indian captain Virat Kohli, who had looked confident in scoring 28 before he was trapped leg before wicket.
Philander struck again when Rohit Sharma was bowled off an inside edge and Rabada dismissed first innings top scorer Hardik Pandya for one, caught by a diving De Villiers at third slip. Rabada trapped Wriddhiman Saha leg before with the last ball before tea to leave India in a desperate situation in a match which hastened to a conclusion despite the loss of the third day because of rain.
Ravichandran Ashwin and Bhuvneshwar Kumar put on 49 for the eighth wicket before Philander took the last three wickets in the space of four balls.
Scoreboard
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South Africa, first innings, 286
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India, first innings, 209
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South Africa, second innings (overnight 65-2)
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A. Markram c Kumar b Pandya 34
D. Elgar c Saha b Pandya 25
K. Rabada c Kohli b Mohammed Shami 5
H. Amla c Sharma b M. Shami 4
A. de Villiers c Kumar b Bumrah 35
F. du Plessis c Saha b Bumrah 0
Q. de Kock c Saha b Bumrah 8
V. Philander lbw b Mohammed Shami 0
K. Maharaj c Saha b Kumar 15
M. Morkel c Saha b Kumar 2
D. Steyn not out 0
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Extras: (w2) 2
Total: (41.2 overs) 130
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Fall of wickets: 1-52 (Markram), 2-59 (Elgar), 3-66 (Amla), 4-73 (Rabada), 5-82 (Du Plessis), 6-92 (De Kock), 7-95 (Philander), 8-122 (Maharaj), 9-130 (Morkel)
Bowling: Kumar 11-5-33-2 (2w), Bumrah 11.2-1-39-3, Mohammed Shami 12-3-28-2, Pandya 6-0-27-2, Ashwin 1-0-3-0
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India, second innings
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M. Vijay c De Villiers b Philander 13
S. Dhawan c sub (Morris) b Morkel 16
C. Pujara c De Kock b Morkel 4
V. Kohli lbw b Philander 28
R. Sharma b Philander 10
W. Saha lbw b Rabada 8
H. Pandya c De Villiers b Rabada 1
R. Ashwin c De Kock b Philander 37
B. Kumar not out 13
Mohammed Shami c Du Plessis b Philander 4
J. Bumrah c Du Plessis b Philander 0
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Extras: (lb1) 1
Total: (42.4 overs) 135
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Fall of wickets: 1-30 (Dhawan), 2-30 (Vijay), 3-39 (Pujara), 4-71 (Kohli), 5-76 (Sharma), 6-77 (Pandya), 7-82 (Saha), 8-131 (Ashwin), 9-135 (Shami)
Bowling: Philander 15.4-4-42-6, Morkel 11-1-39-2, Rabada 12-2-41-2, Maharaj 4-1-12-0
Result: South Africa won by 72 runs
Series: South Africa lead the three-match series 1-0
Toss: South Africa
Umpires: Michael Gough, Richard Kettleborough (both ENG)
TV umpire: Paul Reiffel (AUS)
Match referee: Chris Broad (ENG)
Remaining matches:
January 13-17, Centurion
January 24-28, Johannesburg.