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India set Australia a target of 353 to win their match at The Oval, after belting 116 runs off the last 10 overs on Sunday.
An opening partnership of 127 between Shikhar Dhawan (117) and Rohit Sharma (57) gave India wickets in hand to have a late bash.
Pandya hit three sixes in a 27-ball 48, Kohli was out for 82 off the penultimate ball as India racked up 352/5.
Pandya was dropped on the first ball he faced, when he edged behind Nathan Coulter-Nile and the ball glanced off Alex Carey's gloves diving to the right.
Sharma was dropped on 2 in the second over, a tough chance at mid-wicket as the ball went through Coulter-Nile's high right hand off Mitchell Starc's bowling.
Starc and Pat Cummins, who drew edges off the openers, restricted India to 41/0 in the first 10 overs, but India took control against the change bowlers.
His and Dhawan's century stand was their 16th in ODIs, tied for second in history with Adam Gilchrist and Matthew Hayden, and behind only Sourav Ganguly and Sachin Tendulkar with 21.
Sharma, who scored an unbeaten century in India's opening win against South Africa, fell for 57 from 70 balls. He edged behind a Coulter-Nile riser in the 23rd over.
Dhawan, the aggressor in their partnership, continued imperiously.
He brought up his 17th ODI century, fourth against Australia, and third in the World Cup, on an overthrow.
Kohli's stumps at the non-striker's end were hit by a throw from Cummins. As the ball glanced away, Kohli quickly got back up and completed the single Dhawan needed. Then they had to wait until video confirmed Kohli was not run out.
Dhawan was finally out in the 38th, holing out at deep midwicket. He left to a standing ovation from the ring of overwhelming blue shirts at the Oval.
Kohli appeared on course for a century, but Dhoni replaced Pandya and dominated the strike as he smashed 27 in 14 balls.
Dhoni was out to an outstanding caught-and-bowled dismissal by Marcus Stoinis, and Kohli was caught in the deep soon after. He'd won the toss, and his decision to bat first paid off.
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