Some 199 people died when an airliner skidded off a runway and crashed into a building at São Paulo's Congonhas airport.
Mr Pereira is the second top official to be sacked over the crash, after the defense minister also lost his job.
It was the new defense minister, Nelson Jobim, who requested that Mr Pereira resign and who announced his resignation. The defense ministry supervises civil aviation in Brazil.
Gaudenzi, who should take office this week, is being sued by Brazil's Audit Court (TCU) for his acts as head of the Brazilian Space Agency (AEB).
The TCU argues that he acted illegally when the AEB paid 16 million reais (about US$ 8 million) to the Russia Space Agency to take Brazilian first astronaut, Marcos Pontes, into space, in 2006.
The airports authority, Infraero, has been criticized for allowing the Congonhas runway to be used even though it had not been "grooved" after being surfaced. Grooving helps water escape the surface of the runway.
It had been raining heavily on 17 July, the day of the crash – that is one of several possible contributory factors being analyzed by investigators.
The disaster was the second major air tragedy in Brazil in the space of less than a year. In late 2006, a Gol passenger plane and an executive jet collided over the Amazon, killing 154 people.
Mercopress