Captain Sairaj Bahutule returned impressive figures of 4 for 11 to help the visitors bundle out the Select XI for 131 in their second innings, setting them a mere 25-run winning target.
Openers Dheeraj Jadhav (13) and Gautam Gambhir (12) reached the target in just 8.2 overs on the third day of the four-day match.
Earlier, Ramesh Powar and Shiv Shankar Paul also gave a creditable performance, returning with three wickets for 33 runs and three wickets for 38 runs respectively.
Bahutule also shone with the bat, scoring a fine 57 while Rohan Gavaskar (60) and Dinesh Karthik (52) along with M S Dhoni (45) helped India amass 259 in their first innings on Friday in reply to the hosts' 152.
For Zimbabwe, Tinashe Panyangara returned with fine figures of five for 60 and Test player Mark Vermeulen contributed a defiant 40 in their second innings.
The Indians, who won the first match by nine wickets earlier this week, will play the last match on the tour against Zimbabwe 'A' from August 5.