Continuing a tradition, space station commander Fyodor Yurchikhin rang a bell and said "Atlantis departing."
Pilot Lee Archambault steered Atlantis on a quick trip around the station so photos could be taken of the solar power array the crew installed on the half-built home in space.
Once Atlantis was 46 miles away from the station, astronauts planned to use a camera at the end of a robotic arm and boom for a final inspection of the shuttle's heat shield to make sure it is undamaged and can withstand the intense heat of re-entering Earth's atmosphere.
That inspection was added to all shuttle missions as a safety precaution after the Columbia accident in 2003 that killed seven astronauts.
Atlantis was on schedule to land Thursday at Cape Canaveral, Florida.
It was a busy visit at the space station.
"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," flight director Holly Ridings said Tuesday. "The international space station is in very, very good shape."
Atlantis might have stayed an extra day if engineers hadn't been happy with a test to see how well the Russian computers that crashed last week can control the orbiting outpost's orientation.
Monday's test was a success, said Phil Engelauf, chief of the flight directors' office.
"Yes, we think we're back to where we're supposed to be in terms of normal routine operations and reliability," Engelauf said.
after the shuttle's rocket thrusters were used to re-orient the station for a shuttle waste water dump, reports CBS News space consultant Bill Harwood. When the excess water had been dumped overboard, flight controllers maneuvered the station back to its original orientation, or "attitude," and switched control over to the revived Russian guidance, navigation and control computers. The computers then commanded Russian thrusters to maintain the proper attitude for about an hour.
The computers, revived during the weekend, had not commanded the Russian thrusters since one week earlier, when six computer processors in the two systems started crashing. During the meltdown, Atlantis' thrusters helped maintain the station's orientation.
Engelauf said engineers were still trying to pinpoint the cause of the computer failure.
The computers also control life support systems such as an oxygen generator, temperature, and a carbon dioxide scrubber. Except for the oxygen generator, all the space station systems were turned back on during the weekend. Oxygen for the crews came from other sources, such as a cargo ship on the Russian side of the station.
Atlantis arrived at the space station on June 10.
During four spacewalks, Atlantis' astronauts helped install a new truss segment, unfurled a new pair of power-generating solar arrays, repaired a peeled-back thermal blanket near Atlantis' tail and activated a rotating joint that allows the new solar arrays to track the sun.
The 11-day mission was extended to 13 days so astronauts could repair the thermal blanket.
Twelve more construction missions are needed to finish building the space station before a 2010 deadline, when the shuttles are to be grounded permanently.
The shuttle is bringing back U.S. astronaut and former space station resident Sunita Williams, whose more than six months in space set a record for the longest single spaceflight by a woman. Her replacement, U.S. astronaut Clay Anderson, was taken to the station aboard Atlantis.