Chasing a mammoth victory target of 444, the hosts were happy to bat out the day as they ended at 309 for four when 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, Nair added 148 runs for an unbroken fifth-wicket stand to shut out any chances that the Proteas harboured of a win.
Shankar, on his part, contributed 74 off 142 balls with 12 boundaries to his credit. The duo came together when India were in a bit of trouble at 161 for four in the 64th over of the innings and there was more than 50 overs left in the day at that point of time for the South African side 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. In fact, the duo played first innings' wrecker-in-chief Dane Peidt with a lot of ease.
The off-break bowler managed 1/125 in 43 overs in the second innings and 5/88 in India A's first innings.
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 an aim to draw the match, left-handed 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.
Mukund's four-hour vigil ended with De bruyn taking another close-in catch off Piedt's bowling. However that was the last success that South Africa tasted on the day with both Nair and Shankar batting with a lot of confidence as India A, for the first time, enjoyed upper hand during the final two sessions of the match.