A Colombian Air Force chief described their survival as "a miracle".
Maria Nelly Murillo, 18, and her one-year-old son were found by rescuers near to where their small Cessna plane crashed in Choco province.
Ms Murillo had some injuries and burns while her baby appeared to be in good health.
The twin-engine plane had been flying from Quibdo, the capital of Choco, to the town of Nuqui on the Pacific coast when it crashed in the Alto Baudo region on Saturday. The cause of the crash is not yet known.
Rescuers reached the plane on Monday and found the pilot, Carlos Mario Ceballos, dead in the cockpit.
But the doors of the plane were ajar and Ms Murillo and her baby, Yudier Moreno, were not there.
A 14-person team scoured the jungle for three days before finding them.
"It's a miracle. It is a very wild area and it was a catastrophic accident," Colonel Hector Carrascal of the Colombian Air Force told AFP news agency.
Of the baby, he said: "His mother's spirit must have given him strength to survive."
The couple were airlifted to a hospital in Quibdo.
A young mother and her baby have been found alive five days after their plane crashed in the jungle of western Colombia.