India scored 146 for five, riding on captain Mahendra Singh Dhoni's unbeaten 55 and then Pathan took centre stage with an impressive five for 25 to skittle out the Islanders for 120 in 19.3 overs at the P Sara Oval.
Continuing his fine run, Pathan ripped through the Lankan top order before coming back to dismiss the lower middle order in the end.
The Baroda speedster was ably supported by comeback man Lakshmipathy Balaji, who claimed three for 28.
Set a victory target of 147, Sri Lanka received an early jolt as Pathan castled opener Dilshan Munaweera on the last ball of the first over.
The 27-year-old then dismissed Tillakaratne Dilshan with the last ball of his second over to leave the the hosts reeling at 15 for two from the first three overs.
Kumar Sangakkara (32) combined with Angelo Mathews (16) to resurrect the Lankan innings but with Balaji getting better off the later, the target seemed to be a distant one for the hosts.
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Sangakkara, in company of Lahiru Thirimanne, slowly but steadily took the Lankan total past 70 runs, punishing anything lose dished out by the bowlers.
Their partnership was, however cut short as Harbhajan Singh, dawning the Indian colours after a gap of over an year, bowled Sangakkara out in the 12th over to put India in a driver's seat.