Chasing a mammoth victory target of 444, the hosts battled to 309 for four before the umpires decided to call off the match after consulting the two captains, Ambati Rayudu and Dane Vilas.
The highlight of the final day's play was 23-year-old Nair's unbeaten 114 off 192 balls, which was laced with 18 boundaries and a big six.
In the company of Tamil Nadu all-rounder Vijay Shankar, he added 148 runs for an unbroken fifth-wicket stand to wipe out any hopes the Proteas harboured of victory.
Shankar, on his part, contributed 74 off 142 balls, which included 12 boundaries.
The duo came together when India were in a bit of trouble at 161 for four in the 64th over of the innings and more than 50 overs left in the day for the South Africans to get the remaining six wickets.
The best part about the Nair-Shankar partnership was their positive intent as they added the runs in 43.3 overs.
The duo played first innings' wrecker-in-chief Dane Peidt with a lot of ease. The off-break bowler, who claimed 5 for 88 in the first innings, got just one wicket for 125 runs in 43 overs in the second.
In the morning, the Rayudu-Abhinav Mukund partnership yielded 51 runs before the India ‘A’ captain was snapped up by close-in fielder Theunis de Bruyn off left-arm spinner Keshav Maharaj's bowling.
With the aim to draw the match, left-hand opener Mukund downed the shutters early as he hardly attacked the bowling but at the same time was rock-solid in defence, scoring 65 off 200 balls, with eight boundaries. His four-hour vigil ended with De bruyn taking another close-in catch off Piedt's bowling.
However, that was the last success South Africa tasted on the day as both Nair and Shankar batted with a lot of confidence as India ‘A’, for the first time, enjoyed the upper hand during the final two sessions of the match.
Scoreboard
South Africa ‘A (1st innings):
India ‘A’ (1st innings): 204
South Africa ‘A’ (2nd innings): 105-1 decl.
India ‘A’ (2nd innings): (target: 444 runs)
J Singh run-out (Piedt) 1
A Mukund c de Bruyn b Piedt 65
A Bains b Maharaj 27
A Rayudu c de Bruyn b Maharaj 15
K Nair not out 114
V Shankar not out 74
Extras: (b-6, lb-5, w-1, nb-1) 13
Total: (For 4 wickets; 107.2 overs) 309
Fall of wickets: 1-4, 2-43, 3-94, 4-161
Bowling: Parnell 3-0-19-0, Paterson 21-5-69-0, Maharaj 36-12-79-2, Piedt 43-14-125-1, Van Zyl 4.2-2-6-0.