Rescue officials said Minor Vidal, 35, was found with head injuries away from the site of Tuesday's crash.
Mr Vidal told his rescuers he escaped after being trapped in the wreckage and survived by drinking his own urine and water from a lagoon.
Eight people were killed in the crash near Trinidad, in north-east Bolivia.
The Aerocon Airlines flight was travelling from Santa Cruz to Trinidad when air traffic controllers lost track of it. All nine passengers and crew were originally reported to have been killed in the crash.
The head of the rescue mission, Captain David Bustos, said they began searching further away from the wreckage when they found only eight bodies at the crash site.
"From several kilometres (miles) away, we saw a man on the river bank signalling to us. When we got closer, he knelt down and thanked God," Capt Bustos said.
"He said he'd been trapped in the plane for more than 15 hours and that when he finally escaped he began to walk and survived by drinking his own urine and water from a lagoon," Reuters quoted Capt Bustos as saying.
A Bolivian man who was the sole survivor of a plane crash has been found alive in the Amazon jungle three days after the plane went down.