The medium pacer, whose five for 61 helped India win the fifth one-day international on Saturday, took three wickets for 27 runs to break the back of the Sri Lankan batting.
Sri Lanka never recovered from that early setback and were dismissed for a disappointing 116 runs in 18 overs in reply to India's moderate total of 155 for three as Virat Kohli hammered 68.
Then Pathan gave India the ideal start by shattering the stumps of Tillakaratne Dilshan for a duck and then went on to dismiss Upul Tharanga for five and the Sri Lanka captain Mahela Jayawardene for 26.
Ashok Dinda took four for 19 as Sri Lanka came up well short, with Angelo Mathews top scoring with 31.
"I think we mastered our bowling and batting better than them," said MS Dhoni, the India captain. "We thought we were 15 runs short, but overall we were really good."
India lost Gautam Gambhir in the second over, bowled by Shaminda Eranga - who had already dropped the left-hander.
But Kohli got under way with back-to-back boundaries off Mathews followed by three off Eranga in the next over.
Thisara Perera came in for similar punishment, with three loose deliveries put away consecutively and Ajinkya Rahane hitting him for six in his next over.
Rahane, the opening batsman, was still on only 18 though, when Kohli brought up a 32-ball half-century at the start of the 10th over with his 10th boundary.
He was undeterred by Rahane's dismissal, caught and bowled by Jeevan Mendis for 21, and launched a six later in the same over.
Kohli narrowly escaped being run out but then swatted Eranga straight to Lahiru Thirimanne at midwicket to end his 48-ball onslaught.
Kohli's exquisite innings included 11 fours and one six in his maiden Twenty20 half-century.
Suresh Raina hit Lasith Malinga for six on his way to 34 not out from 25 balls and the India captain MS Dhoni (16 not out) chipped in with two boundaries to keep the momentum going to the end.
A first-ball duck for Dilshan was far from the ideal start for Sri Lanka and Tharanga added only five, leaving them 14 for two.
Jayawardene was going well at the other end and attempted to inject some momentum with four boundaries in one Umesh Yadav over, but he fell victim to a marginal lbw decision when struck on the knee-roll by Pathan.
Thirteen runs came in three balls in Dinda's first over, including four overthrows, but a steady procession of wickets prevented Sri Lanka stepping up their run chase.
Thirimanne (20) missed a reverse sweep at Ravichandran Ashwin and was bowled, Mathews (31) edged Dinda to the wicketkeeper Dhoni and Jeevan Mendis (11) chipped to cover as the hosts stumbled to 100 for six.
Perera was then run out, and although 12 came from Pathan's last over, Dinda ripped out the last three wickets in his third over to polish off the tail and help dismiss the hosts for the lowest score in Twenty20 matches between the two sides.
"We thought 150 was achievable," a disappointed Jayawardene said last night. "We're making a lot of mistakes and when you come across a team like India it is tough."
The tourists also won the five-match one-day series 4-1 to complete their short tour on a high note.
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