Flight directors sought clear skies for one of two landing opportunities at the Kennedy space centre in Florida, the shuttle's home port, but dense clouds and rain prevented it.
Nasa had to forego two landing opportunities in Florida on Thursday as well because of bad weather.
The shuttle had been on a two-week construction mission to the International Space Station, a $100bn project of 16 nations that is a little more than half finished.
Friday's landing came as the clock was ticking, with the shuttle's hydrogen batteries, which provide its electric power, only having one more day of life.
The US space agency would have preferred to land the shuttle in Florida as it costs nearly $2m to return it from California piggy-backed atop a Boeing 747 and this could affect the schedule of future missions.
|Sunita Williams, centre, returned to Earth lying|
prone after 194 days in space [Reuters]
While docked at the International Space Station during their 13-day mission, astronauts successfully installed a new truss segment, expanding the station's laboratory with a new set of power-generating solar arrays.
The astronauts ventured out on four spacewalks to set up the truss and fix a thermal blanket which was damaged when the shuttle shot into orbit.
The small hole in the heat shield prompted concerns for the craft's safety on re-entry, but Nasa declared it fit to return after the repairs.
Engineers stressed it posed no threat to the crew, unlike the broken tile that caused shuttle Columbia to break up on re-entry in February 2003, killing all seven astronauts on board.
Atlantis brings back with it Sunita Williams, who had been on the ISS since December and has set a new record for the longest uninterrupted space flight by a woman.
Williams returned to Earth lying flat on her back in her crew couch, Nasa said. Astronauts often return from long missions lying prone to ease the transition to gravity.
Atlantis left behind one crew member, Clayton Anderson, who is to stay on the orbiting research lab for four months alongside two Russian cosmonauts.
Nasa plans at least 12 more shuttle missions, including three this year, as it races to finish building the International Space Station by 2010, when the space agency retires its three remaining orbiters.
It considers the station a vital part of US ambitions to send a manned mission to Mars.