Tendulkar top-scored with 93 as India, chasing 227 for victory, finished on 227 for four with five balls to spare, and so levelled the three-match series at 1-1.
But India, after a top-order collapse, needed an unbroken fifth-wicket stand of 85 between Yuraj Singh, who'd earlier taken three for 36 with his part-time left spin, and Dinesh Karthik to see them home.
Yuvraj was 49 not out and Karthik 32 not out.
South Africa's total of 226 for six featured a career-best 82 from opener Morne van Wyk, which revived the Proteas after they'd collapsed to seven for two having been sent into bat on a seaming pitch, and a run-a-ball 55 not out from wicket-keeper Mark Boucher.
India, cruising to victory at 134 without loss, then lost four wickets for eight runs in 28 balls.
Tendulkar, who'd needed exactly 50 runs to reach the 15,000 mark when he began his innings, completed his half-century with a single off Nel which became a five after four overthrows. Tendulkar's 79th fifty at this level, in his 387th match, had come in 64 balls with one six and nine fours.
Man-of-the-Match Tendulkar once more fell in sight of a hundred when he bottom-edged an intended cut off Tshabalala onto his stumps. He had faced 106 balls with two sixes and 13 fours.
That left Tendulkar, 34, with a record of 15,043 one-day international runs at an average of 44.24 with 41 hundreds.
Scoreboard
SOUTH AFRICA:
M.N. van Wyk c Dhoni b Yuvraj 82
A.B. de Villiers run out 0
J.H. Kallis b R.P. Singh 2
H.H. Gibbs c Karthik b Zaheer 17
J.P. Duminy c Dravid b Yuvraj 40
M.V. Boucher not out 55
A.J. Hall b Yuvraj 17
A. Nel not out 1
EXTRAS (LB-5, W-5, NB-2) 12
TOTAL (for six wkts, 50 overs) 226
FALL OF WKTS: 1-2, 2-7, 3-46, 4-131, 5-168, 6-220.
DID NOT BAT: T. Tshabalala, C.K. Langeveldt, M. Ntini.
BOWLING: Zaheer Khan 9-2-29-1; R.P. Singh 6-1-21-1 (3w); Sharma 7-0-38-0; Chawla 8-0-41-0; Powar 10-0-46-0; Tendulkar 1-0-10-0 (1w); Yuvraj Singh 9-0-36-3.
INDIA:
S.C. Ganguly c Gibbs b Langeveldt 42
S.R. Tendulkar b Tshabalala 93
R. Dravid c and b Langeveldt 2
Yuvraj Singh not out 49
M.S. Dhoni b Ntini 0
K.D. Karthik not out 32
EXTRAS (LB-2, W-7) 9
TOTAL (for four wkts, 49.1 overs) 227
FALL OF WKTS: 1-134, 2-140, 3-140, 4-142.
DID NOT BAT: Piyush Chawla, R.R. Powar, Zaheer Khan, R.P. Singh, I Sharma.
BOWLING: Ntini 10-1-37-1 (2w); Langeveldt 10-1-43-2; Nel 10-0-41-0 (1w); Hall 10-0-54-0 (1w); Tshabalala 8-2-42-1 (1w); Kallis 1.1-0-8-0 (1w).
RESULT: India won by six wickets.
UMPIRES: B.F. Bowden (New Zealand) and M.R. Benson (England).
TV UMPIRE: Aleem Dar (Pakistan).
MATCH REFEREE: A.G. Hurst (Australia).
MAN-OF-THE-MATCH: Sachin Tendulkar.
FIRST MATCH: South Africa won by four wickets.
THIRD MATCH: On Sunday.—AFP