After a seven-year journey across 4.63 billion kilometers of space, the capsule weighing 46 kilograms and carrying a teaspoonful of space dust landed in the Utah desert at 1010 GMT.
The mission was the first attempt to gather, beyond the Moon, space particles that date back to before our solar system was born, or about 4.5 billion years ago.
"We visited a comet, grabbed a piece of it, and landed here this morning," said Don Brownlee, the principal investigator for the Stardust mission.
"It was a real thrill."
Comets are thought to be leftovers from the process of planet formation, and scientists hope the dust collected by Stardust will give them clues about the origins of the solar system.
Excellent condition
The probe, which had traveled 10,000 times more than the distance separating Earth from the Moon, was in "absolute excellent condition," according to Joe Vellinga, the Stardust program manager for US aeronautics firm Lockheed Martin.
NASA described its entry speed, at 46,444 kilometers per hour, as the fastest ever of any human-made object, topping the record set in May 1969 by the returning Apollo 10 command module.
About four hours after releasing its return capsule, Stardust entered the Earth's atmosphere at about 125 kilometers.
The capsule then released a drogue parachute at approximately 32 kilometers.
"When we saw that drop chute open, we knew we were home safe," said Tom Duxbury, the mission's manager for NASA.
Once the capsule had descended to about three kilometers, its main parachute deployed, leading to a very swift deceleration.
"It's like (being) the parent at the graduation of a cum laude student,” glowed former Stardust project manager Ken Atkins.
"We had a great navigation and engineering team."
Television images showed scientists and engineers in the control room at NASA's Jet Propulsion Laboratory in Pasadena, California, cheering and applauding.
"This thing went like clockwork," Mr Tom Duxbury said.
"To see that thing in one piece on the floor of the desert is very moving," he added.
Less than an hour after the landing, three helicopters retrieved the capsule from the windy and dark desert floor, helped by infrared and radar tracking devices.
Recovery of the muddied but intact capsule took slightly longer than expected, officials said, because heavy winds blew it north of its exact target.
The vessel was taken to a "clean room" at the base where the canister containing the particles will be removed from the capsule before being shipped to Johnson Space Centre in Houston for scientists to study.
"Much of the science of this mission hasn't been done yet," Mr Brownlee said.
Long journey home
The Stardust probe, weighing 385 kilograms, was launched in 1999.
It circled the Sun twice and then flew by comet Wild 2 in January 2004, which at the time was located next to Jupiter.
During its hazardous traverse, the spacecraft first deployed a shield to protect itself from gases and space dust contained in the halo of the comet.
It then flew within 240 kilometers of Wild 2, catching samples of comet particles and taking detailed pictures of Wild 2's pockmarked surface.
The 72 pictures of Wild 2 taken by the probe show its rugged surface, including craters as well as about 20 "geysers" spewing gas and dust.
During 195 days of the flight, NASA engineers used a collector to gather interstellar dust that will also allow scientists to study the make-up of stars.
The special collector contains aerogel, a unique substance that can trap the particles and store the precious cargo safely for the trip back to Earth.
The particles, most of which are expected to be a tenth as wide as a piece of human hair, lodged in the aerogel before being shuttered inside the capsule.
Analysing the stardust
The mission marks the first time since 1972 that any extraterrestrial solid material has been collected and brought back to Earth, and the first time ever for comet particles.
Painstaking analysis could take scientists as long as 10 years.
The work, according to one scientist, could be compared to finding 45 ants on a football field, or studying five square centimeters of earth at a time.
To help the researchers, the University of California, Berkeley, has launched a drive to recruit 30,000 volunteer students, who will have access to a powerful microscope via the Internet.
Stardust's mother ship, which severed the umbilical cables between it and the capsule late yesterday, returned to orbit around the sun and may be used in future missions to study planets, asteroids or comets.