Woman identified as Maria Nelly Murillo, 18, and her one-year-old son had been flying from Quibdo, the capital of Choco, to the town of Nuqui on the Pacific coast when twin-engine plane crashed in the Alto Baudo region on Saturday, BBC reported.
Their survival has been described as miracle by an official of the Colombian air force chief.
They were rescued near to where their small Cessna plane crashed in Choco province.
Mother survived with some injuries and burns while her baby appeared to be in good health.
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 Murillo and her baby, Yudier Moreno, were not there.
A 14-person team scoured the jungle for three days before finding them. Duo were airlifted to a hospital in Quibdo.