Sri Lanka lost 5-0 to India and Pakistan in recent one-day series.
They are currently playing a three-test series in India which will be followed by a three ODIs and the same number of T20 internationals.
"We are keen to implement our selections policy across the board in all aspects of the game, and Thisara's appointment is one such move," Sri Lanka chief selector Graeme Labrooy said in a statement.
"We believe this is the leadership skillset the team needs right now, and have made this decision specifically with our long term goals in mind.
"Tharanga had not failed us in anyway, we want him to keep making big scores and want him to concentrate on his game without burdening him with the captaincy."
While Dinesh Chandimal leads Sri Lanka in tests, they have failed to find a solution to the captaincy issue in limited-overs cricket since long-serving skipper Angelo Mathews stepped down following the team's first ODI series loss to Zimbabwe earlier this year.
Perera captained Sri Lanka against Pakistan in last month's three-match T20 series.
"All teams go through tough patches, it's up to each of us to get past our mental barriers and perform best for our country," Perera said.
(Reporting by Sudipto Ganguly in Mumbai; editing by Ed Osmond)
