The hosts won the third T20 by 14 runs in Dambulla on Sunday.
In a rain-reduced match, Sri Lanka captain Dasun Shanaka smashed five sixes in 34 runs off nine balls that propelled Sri Lanka to a strong 6-160 in their allotted 12 overs after Pakistan had won the toss.
Pakistan skipper Salman Ali Agha matched his counterpart with a blistering 45 off just 12 balls before Sri Lanka fast bowlers Matheesha Pathirana (2-34) and Eshan Malinga (1-27) bowled two tidy overs at the end and restricted the visitors to 8-146.
Pakistan won the first T20 by six wickets before the second game was washed out without a ball being bowled in Dambulla.
The series was part of both teams' preparations for next month's T20 World Cup to be jointly hosted by India and Sri Lanka. Pakistan are due to play all their World Cup games in Sri Lanka.
Agha had slashed the target to 101 inside the first four overs of Pakistan's lively chase when he smacked three sixes and five fours. But Pathirana provided a crucial breakthrough when Agha holed out to short fine leg while attempting a ramp shot against the pacer.
Key wrist-spinner Wanindu Hasaranga (4-35) then picked up two wickets in his first five deliveries — Saim Ayub and Usman Khan were caught in the outfield as Pakistan slipped to 4-67.
Mohammad Nawaz (28) and debutant wicketkeeper-batter Khawaja Nafay (26) revived the chase with a breezy 49-run stand before Hasaranga grabbed two more wickets in his final over.
With 30 needed off the final two overs, Pathirana clean bowled Nawaz with a slower delivery in the penultimate over which went for 10 runs. Malinga's final over conceded just five runs, including four wides.
It was Sri Lanka's first T20 win against Pakistan at home since 2012.
Sri Lanka's top-order batters earlier kept scoring at a rapid pace in challenging conditions for the bowlers, who had to bowl with the wet ball due to soggy outfield.
Opener Kamil Mishara scored 20 off 8 balls; Kusal Mendis capitalised on a dropped catch with a knock of 30 off 16; and former white-ball captain Charith Asalanka scored 21 off 13.
Shanaka and Janith Liyanage (22 not out off 8 balls) provided the late flurry as Sri Lanka scored 58 runs in the final three overs - 19 runs in the 10th over, 15 in the 11th and 24 in the 12th.
Shanaka stayed deep in his crease and smacked Wasim for three successive sixes in the last over.
Pakistan will play a three-match T20 series against Australia at home before the T20 World Cup begins February 7 while Sri Lanka hosts England in a white-ball series later this month.
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