"Marvan aggravated the injury while fielding in the first match on Friday and the medical staff have advised us to rest him for the One-dayers as well as the Tests," chief selector Lalith Kaluperuma told AFP on Saturday.
Atapattu's back injury added to the home side's woes as star batsman Sanath Jayasuriya (thigh), ace seamer Chaminda Vaas (side strain) and paceman Ruchira Perera (hamstring) are already nursing injuries.
Atapattu, who sustained the injury during the tour of Australia in January, aggravated it on Friday. Recurring back problems have frequently kept him on the injured list of late.
The selectors will not name a replacement for Atapattu and his deputy Mahela Jayawardene will lead the side.
The remaining One-dayers will be played here on Sunday and Wednesday with provisions for reserve days after the opening match was abandoned due to rain. They will be followed by two Tests with Colombo and Kandy as the venues.