On Friday, Voepass said the plane was carrying 57 passengers and four crew, but on Saturday the firm confirmed another unaccounted-for passenger had been on the flight, putting the number of casualties at 62.
Authorities are using seat assignments, physical characteristics, documents and belongings such as cell phones to identify the victims, firefighter Maycon Cristo said at the crash site earlier on Saturday as the bodies were being pulled from the wreckage.
Relatives of the victims were brought to Sao Paulo to provide DNA samples to aid in identification of the remains, said state civil defense coordinator Henguel Pereira.
The plane's so-called "black box" containing voice recordings and flight data was undergoing analysis, said Marcelo Moreno, the head of Brazilian aviation accident investigation center Cenipa, at a press conference in Vinhedo.
The plane, an ATR-72 turboprop, was bound for Sao Paulo from Cascavel, in the state of Parana, and crashed around 1:30 p.m. (1630 GMT) in Vinhedo, some 80 km (50 miles) northwest of Sao Paulo. Despite coming down in a residential area, no one on the ground was hurt.
The aircraft was flying normally until 1:21 p.m., when it stopped responding to calls, and radar contact was lost at 1:22 p.m., Brazil's air force said in a statement.
Pilots did not report an emergency or adverse weather conditions, the air force added.
Franco-Italian ATR, jointly owned by Airbus and Leonardo, is the dominant producer of regional turboprop planes seating 40 to 70 people. ATR told Reuters on Friday that its specialists were "fully engaged" with the investigation into the crash.