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Three of India's top four batsmen scored 70 or more as the hosts chased down a 294-run victory target with 13 balls to spare for their third successive victory in the five-match series.
Earlier, Aaron Finch smashed 124 on his return but Australia, cruising at 224-1 at one stage, suffered a mini-collapse to settle for 293-6 in the Holkar Stadium.
India's ninth consecutive ODI win also ensured they are now the top ranked team both in tests and the one-day format.
Bangalore hosts the fourth match on Thursday.
Australia captain Steve Smith won the toss for the first time in the series and opted to bat first.
Openers Finch and David Warner give Australia a solid, if not spectacular, start with a 70-run stand as the tourists looked determined to preserve wickets.
Pandya bowled Warner for 42 but Finch and Smith added 154 runs for the second wicket with a 325-plus total looking well within Australia's reach.
If Finch, who smacked five sixes and 12 boundaries in his nearly run-a-ball knock, plundered his runs, Smith accumulated them quietly, hitting five boundaries in his 63.
Left-arm wrist-spinner Kuldeep Yadav dismissed both to trigger a collapse as Australia lost five wickets for 51 runs to fall short of the 300-mark.
India reached the 100 mark in 15 overs without losing a wicket, Rohit Sharma leading their robust reply with a blistering 71.
The opener smacked four sixes, one of them sailed over the stadium, as he and Ajinkya Rahane (70) scored 139 runs to take the hosts nearly halfway down the target.
India soon suffered a mini-collapse of their own, losing four wickets, including their openers and skipper Virat Kohli, for 67 runs.
Batting at number four, Pandya hit four sixes and five boundaries in his aggressive knock to take India close to victory.
Manish Pandey completed the formality with a quickfire 36 not out to see his side home.