The shuttle undocked at about 10:40 a.m. ET, and touchdown at Cape Canaveral, Fla., is planned for Thursday afternoon.
"There were a lot of things to overcome, but despite those surprises, we managed to do what we always do and meet our mission objectives," said flight director Holly Ridings, reported the Associated Press.
The problems began with the need to repair a part of the thermal blanket on the tail of Atlantis that peeled back after the shuttle launched. Astronaut Danny Olivas used a surgical stapler and stainless steel pins to put the blanket back in place.
Then, six computer processors in the Russian thrusters that handle navigation and control of the space station began crashing. The computers, revived during the weekend, were successfully tested Monday. During the meltdown, Atlantis' thrusters helped maintain the station's orientation, according to the AP.
During several spacewalks, the astronauts also helped install a truss segment to the space station, unfurled a pair of power-generating solar arrays and activated a rotating joint that lets the new solar arrays track the sun.
Twelve more missions are needed to finish constructing the space station before a 2010 deadline when the shuttles are set to be taken out of service.
Atlantis is ferrying back to Earth U.S. astronaut Sunita Williams, who spent more than six months on the orbital outpost, setting the record for the longest single spaceflight by a woman. She was replaced by U.S. astronaut Clay Anderson.
Other astronauts on board the Atlantis are Commander Frederick Sturckow, pilot Lee Archambault, and mission specialists James Reilly II, Steven Swanson and Patrick Forrester.