Pandey anchored the chase hitting an unbeaten 93 off 85 balls as India A chased down a tricky target of 267 with two balls to spare. All-rounder Krunal Pandya's 25 off 15 balls was also a significant contribution in the end.
This was India A's third successive win in the tournament and playing the final is just a mere formality.
The other useful contribution was Sanju Samson's patient 68 off 90 balls.
India A were in trouble at 225 for 7 when Yuzvendra Chahal (17) got out after a 43-run stand with Pandey.
However, Krunal came in and blasted three fours and a six, contributing 25 out of the 35 runs that the duo put on in 3.5 overs as the match swung in India A's favour.
India needed 4 runs off 9 balls when No 10 Siddharth Kaul was dismissed.
However, Pandey kept his cool in company of last man Mohammed Shiraz (2 no) as they got the winning runs off Carl Dala's final over.
Pandey hit five fours and two sixes in his innings.
He is all set to make a comeback into the Indian team for the limited overs series in Sri Lanka after scores of 55, 41 no, 86 no and 93 no. He has scored 275 runs in four matches getting out only once so far.
Earlier, put into bat, South Africa A were down in the dumps at 128 for six before wicketkeeper-batsman Heinrich Klaasen (127 off 108 balls) and Willem Mulder (66 off 81 balls) added 111 runs to steer the team to a respectable total.
For India A, Shardul Thakur (4/35) and Siddharth Kaul (3/41) were the main wicket-takers.
Brief Scores: South Africa A 266 (Heinrich Klaasen 127, Willem Mulder 66, Shardul Thakur 4/35, Siddharth Kaul 3/41)
India A 267/9 in 49.4 overs (Manish Pandey 93 no, Sanju Samson 68, Krunal Pandya 25 no). India A won by 1 wicket.
First Published: August 3, 2017, 9:40 PM IST