Indian bowlers Ravi Bishnoi and Hardik Pamdya shared five wickets between them to check Sri Lanka's early charge at Kandy's Pallekele International Stadium.
India started with a 43-run win in the opener in Kandy on Saturday to lead the three-match series 1-0 and begin a new era under Suryakumar Yadav and coach Gautam Gambhir.
Suryakumar won a delayed toss due to rain and invited Sri Lanka, led by Charith Asalanka, to bat first.
India struck an early blow with the dismissal of Kusal Mendis for 10 before the right-left handed partnership of Pathum Nissanka, who made 32, Perera, who hit 53, added put on 54 in quick time.
Nissanka departed after being trapped lbw off Ravi Bishnoi but Perera kept up the attack as he raised his fifty with a six off Pandya.
Pandya, a fast bowler who lost out in the T20 captaincy race to Suryakumar, struck twice in one over including Perera to pull things back in India's favour.
Former captain Dasun Shanaka fell bowled to Bishnoi's leg-spin for a second successive first-ball duck.
Bishnoi removed Wanindu Hasaranga next ball but Ramesh Mendis saw off the hat-trick.
Sri Lanka collapsed from 130-2 to 140-6 and lost three further wickets, including two in the final over by Axar Patel.
India have made a fresh start to their T20 journey after the retirements of stalwarts Rohit Sharma, Virat Kohli and Ravindra Jadeja from the format following their World Cup triumph last month.
Sri Lanka also made changes to their set up after an early exit from the T20 World Cup and named Asalanka as captain and Sanath Jayasuriya interim coach.
