They successfully restored electrical power to the craft and boosted its orbit to stop it spiralling back to Earth.
Throughout Sunday, Nasa had thought that the crosswind might be too strong for a safe landing at Kennedy Space Center, Florida.
But the wind eased to within safety limits, and Mission Control gave the crew the go-ahead to come home.
Atlantis glided onto the floodlit runway - it was only the 14th time in 98 flights that a space shuttle has landed in darkness.
Congratulations
Commander James Halsell Jr had used both orbital-manoeuvering engines for the ride home.
The left engine seemed to have a stuck valve during the climb to orbit on 19 May, but flight controllers later concluded the valve was fine and a bad sensor was to blame.
After the hectic pace of the past 10 days, the astronauts said they would have liked an extra day or two in space with little to do.
"As one person who is getting mentally prepared to spend six months up here, I think any extra day is a good thing," said Susan Helms, a future space station resident.
New batteries
Susan Helms and Russian crewmate Yuri Usachev had the most important job of the mission: replacing four bad batteries inside the international space station.
The seven-member crew also furnished the ISS with a new antenna, construction crane, fire extinguishers, smoke detectors and fans, and boosted the complex into a higher orbit.
Susan Helms and astronaut James Voss said they were impressed with the space station, which next year will become their home.
"I think it's a place, after being here for about a week, that I'll be able to live for 5½ months," Mr Voss said during a news conference late on Saturday.
Before anyone can move in, the Russians must launch the Zvezda service module and its life-support systems.
It is due in July after more than two years of delay.
Even if it is postponed again, the space station is now equipped to fly solo through the end of this year.