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.

The United States-born 21-year-old was with Dumbarton last season.
"I am excited about the year ahead as I have forced my way into the Republic of Ireland U21s starting XI," he said.
"I was number two for a few years. Hopefully I can keep my spot and get some caps under my belt, which will be a great experience."
Rogers has yet to break into the Dons first team and Danny Ward has arrived on loan from Liverpool to challenge Jamie Langfield and Scott Brown for a starting place at Pittodrie.
So the goalkeeper, who has played three times for Republic of Ireland Under-21s and played 36 times for Dumbarton, was happy to leave on a third loan spell, having also played for Airdrieonians.
"I feel, at this stage of my career, it is important to try and play on a regular basis and going to Falkirk will hopefully give me that opportunity," he told Aberdeen's website.
"It is up to me to go to Falkirk and do well and then to come back next season to Aberdeen and challenge for that number one jersey.
"I feel my career is going in the right direction and I just need to keep working hard.
"Falkirk are a big club who have big expectations and had a good season last year and will be looking to kick on this year."
Falkirk manager Peter Houston told his club website that he regards Rogers as "a fantastic prospect".
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.
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Aberdeen goalkeeper Danny Rogers hopes returning to the Scottish Championship on a season-long loan with Falkirk will boost his international chances.