The 30-year-old sustained suffered a grade one hamstring tear during his side's second T20I against India at the Holkar Stadium in Indore, where the hosts went on to win by 88 runs to clinch the three-match series 2-0 with a game to spare.
Mathews did not come out to bat at all after the injury while delivering his third ball of the third over - 12th in the Indian innings, ESPNcricinfo reported.
Confirming the news, Sri Lanka's team management said that the injury would not only rule out Mathews out of the inconsequential third T20I against India, but will also put him out of action for at least two weeks.
The injury means Mathews will also remain doubtful for the start of the forthcoming Bangladesh tour.
The right-arm medium pacer has a history of suffering hamstring, calf and ankle injuries.
In January this year, he was forced to return home early from the tour of South Africa before remaining out of action for another five months.
Mathews made his return from injury lay-off during his side's Champions Trophy campaign in England, where he featured only as a specialist batsman.
Not only this, Mathews once against suffered a calf injury during a practice session, ahead of the series against Pakistan in UAE in September, and was subsequently ruled out for eight weeks before making a return in India.(ANI)