Rabada.
India slipped into further trouble when skipper Mahendra Singh Dhoni was caught behind off Morkel for five to make it 67-5 in the 12th over.
Tahir, who shared the new ball with Kyle Abbott, dismissed Raina and the recalled Harbhajan Singh off consecutive deliveries in his third over, reducing India to 69-7.
The tail failed to play out the allotted overs against the sustained pressure applied by South Africa.
Ashwin had Amla caught at leg-slip, forced du Plessis to hole out in the deep and bowled de Villiers with a straight ball, but none of the other bowlers worried the tourists.
JP Duminy remained unbeaten on 30, hitting the winning boundary off Suresh Raina.
After the T20 series, South Africa will play five One-day Internationals and four Tests on their 10-week tour of India.
Score Board
South Africa won toss
India
R G Sharma run out 22
S Dhawan lbw b Morris 11
V Kohli run out 1
S K Raina c Amla b Imran 22
A T Rayudu b Rabada 0
*†M S Dhoni c de Villiers b Morkel 5
A R Patel c du Plessis b Morkel 9
Harbhajan Singh b Imran 0
R Ashwin b Morris 11
B Kumar b Morkel 0
M M Sharma not out 0
Extras (lb 1, w 9, nb 1) 11
Total (all out; 17.2 overs) 92
Fall: 1-28, 2-30, 3-43, 4-45, 5-67, 6-69, 7-69, 8-85, 9-85, 10-92
Bowling: Abbott 3-0-21-0 (1nb, 4w); Imran 4-0-24-2 (1w); Rabada 4-0-18-1 (3w); Morris 2.2-0-16-2 (1w); Morkel 4-0-12-3
South Africa
†A B de Villiers b Ashwin 19
H M Amla c R Sharma b Ashwin 2
*F du Plessis c M Sharma b Ashwin 16
J P Duminy not out 30
F Behardien lbw b Patel 11
D A Miller not out 10
Extras (lb 3, w 5) 8
Total (4 wickets; 17.1 overs) 96
Did not bat: J A Morkel, C H Morris, K Rabada, K J Abbott, Imran Tahir
Fall: 1-13, 2-38, 3-49, 4-76
Bowling: Kumar 2-0-13-0 (1w); Ashwin 4-0-24-3; Harbhajan 4-0-20-0 (2w); M Sharma 1-0-7-0; Raina 3.1-0-12-0; Patel 3-0-17-1
Result: South Africa won by 6 wickets
Series: South Africa lead the 3-match series by 2-0
Man of the Match: J A Morkel (SA)
Umpires: C K Nandan and C Shamshuddin. TV umpire: V A Kulkarni. Match referee: B C Broad (England)