The left-arm seamer bagged four for 59 as West Indies A conceded the match at 242 for nine in their second innings in the 13th over after lunch on the final day at KSCA Stadium.
Wicketkeeper Jahmar Hamilton did not come out to bat due to injury he sustained yesterday while fielding.
The highlight of India's performance was skipper Cheteshwar Pujara's magnificent 306 not out and Gautam Gambhir's 123 which enabled India A to post a mammoth 564 for nine declared in their first innings, thereby ensuring a 296 runs lead.
Zaheer, who finished the match with five for 92 runs, ran into the lower-order batsmen after lunch today in his fourth spell of the innings, claiming three wickets in a space of his eight deliveries.
The 35-year-old started the spell by first cleaning up a dogged Narasingh Deonaraine with a beatiful ball which pierced the defence of the Guyanese after he had made a fighting 99 runs, which included 13 hits to the fence.
Zaheer ran in hard and castled the wickets of Ashley Nurse (0) and Miguel Cummins in his 17th over to help India A seal the Test and level the series.