Agarwal (176 runs off 133 balls) and Pandey (108 not out off 85) shared a 203-run stand for the second wicket to set up a mammoth 371 for three in the crucial clash.
South Africa, who had a rather improbable task of overcoming the massive total in 175 balls to make the final, fought through opener Quinton de Kock (113 off 86), Reeza Hendricks (76 off 109) and Khaya Zondo (86 off 60) before ending at 337 for six in 50 overs.
South Africa's move to field first backfired with India openers Agarwal and captain Unmukt Chand (64 off 77) sharing a century stand to set up the huge total.
It turned out to be a run riot after Chand departed with India at 106 for one in the 22nd over.
Both Agarwal and Pandey, who represent Karnataka on the domestic circuit, toyed with the opposition bowling to complete their 203 run partnership in 24 overs.
Agarwal hammered 20 boundaries and five sixes in his blazing innings, reaching his second straight hundred against South Africa A in the process. The 24-year-old had made 130 in his team's successful chase earlier in the tournament.
It was a second successive fifty plus innings for Pandey and three in a row for Agarwal.
The spirited South Africans surely made a match out of it even though they were never in the hunt for a miracle chase in 175 balls.
De Kock, one of the 10 players to have been hospitalised due to food poisoning earlier in the competition, gave South Africa a glimmer of hope with his entertaining hundred that comprised 10 fours and six sixes.
Hendricks formed a handy pairing with Zondo but his departure meant it was all but over for the touring team.
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