They found the first two bodies at the crash site in the Amazon jungle before halting their search when night fell, a statement from the Brazilian air force said on Sunday. The corpses were loaded on to helicopters and taken to an air force base.
All 149 passengers and six crew on board had been killed, the air force said, confirming what had been feared.
The head of the aviation authority, Milton Zuanazzi, said he did not know how long it would take to recover all the bodies from the crash site in Mato Grosso state, about 1,000km northwest of Brasilia.
Meanwhile, authorities were questioning the seven passengers and crew members who were on an executive jet that made an emergency landing after some sort of collision with the Boeing 737-800 operated by Gol, a low-cost airline.
The executive jet, a Brazilian-made Legacy, had a damaged wing and tail, but landed safely at the Serra do Cachimbo Air Force Base.
All seven passengers, who were identified as Americans heading to the US, said they had felt a bump before the aircraft shook and the pilot took manual control for the landing.
Luiz Inacio Lula da Silva, the Brazilian president, declared three days of official mourning after the crash.
Silva said in a statement: "Brazil is suffering with this. I believe it is the worst aviation accident ever in our country."
Previously, the deadliest crash in Brazil had been in 1982 when a Boeing 727 operated by the now-defunct Vasp airline went down in the northeastern city of Fortaleza, killing 137 people.