After the tourists were sent in to bat, the pair put on 112 for the first wicket as India posted 271 for eight in their 50 overs.
Zimbabwe found quick scoring difficult from the start of their reply and were eventually bowled out for 209 with an over remaining in their innings.
Captain Rahane took 83 balls for his score of 63, while Vijay managed just three boundaries, two of them sixes, as he top-scored for India with 72 from 95 balls.
They were the only two half-centuries of the innings and after they departed India lost wickets at regular intervals on the slow pitch.
Zimbabwe seamer Neville Madziva posted career best figures in all List A matches of four for 49 in his 10 overs.
The home side stumbled in their reply and when their century hero from Friday’s narrow four-run loss, skipper Elton Chigumbura, was dismissed for nine they had slumped to 43 for three in the 11th over.
Opener Chamu Chibhabha provided lone resistance with a neatly compiled 72 from 100 balls before he was run out by a direct hit from Rahane.
Experienced spinner Harbhajan Singh, who has returned to 50-over international cricket after an absence of four years for this tour, bowled tidily to register one for 29 in his 10 overs.
But the pick of the Indian bowlers was medium pacer Bhuvneshwar Kumar with four for 33 from his allotted overs.
The final match of the series will be staged at the same venue on Tuesday, before the teams play two Twenty20 games starting on Friday.
(Reporting by Nick Said; Editing by Ken Ferris)
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