The balloon was part of a research project by academics and students at the University of California, Berkeley, and several Taiwanese universities designed to study gamma rays in space from 25 miles (40 kilometers) above the Earth.
As the huge balloon filled with air, it ripped from its mooring and dragged across the desert, crashing into and upturning a parked four-wheel-drive vehicle and strewing debris across a wide area before coming to a halt.
No one was injured in the accident, which was captured on video by an Australian Broadcasting Corp. television film crew.
Alice Springs couple Stan and Betty Davies were in their car when the gondola broke free and came lurching toward them, hitting the vehicle next to them.
"We were sitting in our car and preparing to move it out of the way and we were actually within about a foot of being wiped out," Betty Davies told the ABC.
The exact cause of the crash was not immediately known, though wind gusts were suspected.
Ravi Sood, an astrophysicist from the University of New South Wales who was overseeing the balloon launch, said quick-changing wind conditions can cause difficulties for launching such large balloons.
"That's the way it happens on occasions but it is very, very disappointing. Gut-wrenching actually," Sood was quoted as saying by ABC.
Equipment was being recovered from the site, and Sood said the team hoped to try again next month.