The two craft came together 220 miles above the Pacific, between Australia and Tasmania.
Astronaut Nicole Stott, a space station resident for the past 2½ months, was thrilled to see her ride home. She spotted Atlantis from three miles out.
"I have my ticket all ready and stamped, waiting for you guys when you get here," Stott radioed to shuttle commander Charles Hobaugh.
"Who is this?" Hobaugh teased.
"It's your favorite passenger," she replied. "You look beautiful out there."
Just before docking, Hobaugh guided Atlantis through a pirouette for the space station cameras, for a final check to make sure there's no damage to the thermal tiles on its belly.
So far, all indications are the shuttle made it through Monday's liftoff just fine, NASA officials said. The astronauts surveyed their ship Tuesday for any signs of launch damage, and a quick look at the laser images shows everything in good shape. Experts will continue to analyze the data, as well as the couple hundred digital photos that were taken Wednesday.
Atlantis will remain at the orbiting outpost until the day before Thanksgiving, enough time for the two crews - 12 astronauts total - to unload nearly 15 tons of spare parts.
Stott, the only woman, greeted Hobaugh with a kiss on the cheek once the hatches swung open. She promptly became a member of the shuttle crew. The space station staff fell to five.
Atlantis is dropping off pumps, tanks, gyroscopes and other huge spare parts for the orbiting outpost, as well as some small, fragile science experiments. Perhaps the most delicate are four butterfly larvae, a student experiment. The plan is for the larvae to develop into Painted Lady butterflies over the next week or two and return on the next shuttle flight in February.
The first of three spacewalks will take place Thursday.
NASA is stockpiling the space station with as much equipment as possible, taking advantage of the spacious shuttle payload bay while it can. Once the shuttles are retired next fall, the orbiting complex will lose its biggest supplier. Officials hope to keep the station operating until 2015, possibly 2020 if President Barack Obama gives the go ahead.
Five shuttle missions remain after this one. NASA is still awaiting word from the White House on what happens after that.
In a jab at the uncertain future, Mission Control sent up a cartoon to Atlantis' crew that showed an astronaut standing, helmet in hand, alongside a landed shuttle. A bureaucrat is telling the newly returned spaceman, "Sorry. Just because you have 20 million miles on your odometer and a few loose tiles on your '74 vehicle, it doesn't make you eligible for the cash for clunkers program."