The US space agency said General Purpose Computer (GPC) 4 "was being used as the systems management computer when it failed at 6:07 pm EDT (2207 GMT) yesterday, generating an alarm that awakened the Atlantis crew."
Shuttle commander Chris Ferguson configured another GPC as the systems management computer before going back to sleep 45 minutes later, NASA said. The agency later announced that the crew had reloaded software into GPC 4 and that it was "operating normally."
"Mission Control is evaluating the `dump` of data from the computer that Atlantis transmitted earlier this morning to determine what caused yesterday evening failure," it said in a statement.
Ferguson later played down the incident in an interview on NASA TV, saying there had been some "minor glitches" with the computer.
"We`re very optimistic it`s going to work for reentry," he added.
NASA had earlier said that a fifth GPC with backup software was available to be used should there be an "endemic problem" with one of the primary computers.
Atlantis is docked at the International Space Station on the final mission of the 30-year US shuttle program and is set to return to earth on July 21.