The astronauts switched to another of the shuttle's five main computers, and Nasa said the shuttle was in "stable condition with no concerns for the crew's safety".
A computer had also failed on Sunday.
The crew had gone to bed late on Thursday afternoon, but Mission Control woke them up about one and a half hours later because of the computer trouble. Nasa said they would troubleshoot the problem.
Sunday's computer failure occurred just before the shuttle linked up with the International Space Station. Engineers said the problem was likely caused by a bad switch throw. That computer was working again after new software was installed.
The check-and-balance network of computers provides redundancy during the most critical phases of the mission, and will be needed when Atlantis lands next week to wrap up the 30-year shuttle era.
Earlier on Thursday, the crew got some time off after a hectic week to savour their historic experience.
Until Thursday, the workload in orbit was so intense that the four astronauts had only fleeting moments of realising "wow, this is really it", astronaut Rex Walheim said in a series of TV interviews.
Atlantis first rocketed into orbit in 1985. This is its 33rd flight and the 135th shuttle mission overall. Atlantis will join Discovery and Endeavour in retirement, following its landing next week.
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