The group said they came across the wreckage at an altitude of about 10,500ft about 350km south of Santiago. Expedition member Leonardo Albornoz said they are keeping the exact site secret to prevent looting.
The disappearance of the Douglas DC-3, carrying members of the top-flight Chilean team Green Cross on April 3, 1961, was one of the great unsolved mysteries in the country.
The club had played an away match in Osorno in the Copa de Chile and was returning to Santiago. The team and staff were spread over two flights. One of the planes reached the capital but the other apparently vanished. Rescuers spent weeks searching for the plane and symbolic funerals for the missing players drew huge crowds in Chile.
“It was a breathtaking moment and we felt all kinds of sensations. One could feel the energy of the place and breathe the pain,” Albornoz said of discovering the wreckage.
The mountaineers said they could see a good part of the fuselage without needing to dig it out.