Iyer (140 not out off 131 balls), who did not score a half century in four round robin games, anchored the chase alongside Tamil Nadu captain Vijay Shankar (72 off 86) to guide India 'A' to victory in 46.5 overs
Earlier, South Africa 'A' recovered to post a competitive 267 for seven after losing half of their side for 115 in the 28th over.
South Africa senior international Farhaan Behardien struck an unbeaten 101 off 114 balls, which eventually went in vain. Dewald Pretorious too played a role in his team's recovery scoring 58 off 61 balls.
India 'A' captain Manish Pandey (32 not out off 38) was amongst the runs once again and took his team past the finishing line.
With scores of 93 not out, 86 not out, 41 not out and 55 in the round robin stage, Pandey is set to return to the India's limited overs side for the Sri Lanka series later this month after not being part of the West Indies tour due to injury.
Both India 'A' and South Africa 'A' had played each other twice in the league stage with either team sharing the spoils.
Chasing 268, India 'A' lost Karun Nair and Sanju Samson early with pacer Junior Dala removing the openers.
Iyer and Shankar then shared a 141-run stand for the third wicket to set up the win.
Iyer, who had scores of 0 and 9 in the earlier games against South Africa 'A', was on song in the title clash smashing 11 boundaries and four sixes.
He completed his century with a maximum before hitting the winning four.
Among the India 'A' bowlers, Shardul Thakur struck thrice while fellow pacer Siddarth Kaul took a couple of wickets after Pandey opted to put the opposition in.
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