South African AB de Villiers holds the record for the fastest ODI fifty, reaching the mark in 16 balls during his blistering 44-ball knock of 149 against West Indies in Johannesburg earlier this year.
Perera's compatriot Sanath Jayasuriya had also scored a 17-ball fifty against Pakistan in Singapore in 1996.
Opting to bat first, Pakistan found the going tough against the home side's disciplined bowling and looked in trouble at 96-3 in the 24th over.
Captain Azhar Ali (79) and Shoaib Malik (51) provided stability in the middle before Mohammad Rizwan hit a quickfire 52 to help Pakistan post 287-8.
Sri Lanka's debutant left-arm spinner Sachith Pathirana dismissed Ahmed Shehzad and Mohammad Hafeez to peg back Pakistan before Ali and Malik rebuilt the innings with an 83-run stand.
Sri Lanka captain Angelo Mathews ended Malik's run-a-ball knock by clean bowling him and Ali fell soon after.
Rizwan provided the late charge with his 38-ball knock as Pakistan scored 88 runs off the last 10 overs to post a competitive total.
Sri Lanka's chase got off to a flying start with Perera and Tillakaratne Dilshan (47) adding 92 runs before being separated in the ninth over.
The hosts lost three quick wickets to find themselves in trouble at the halfway mark of their innings but Pathirana made 33 on debut and Dinesh Chandimal remained not out on 48 to guide them home.
The teams move to Colombo for the third ODI on Sunday.
(Reporting by Amlan Chakraborty in New Delhi; editing by Toby Davis)
