The Mexican, having his last race with the Woking-based outfit, had been due to start 14th at Interlagos.
He achieved that despite crashing into the barriers at Turn 5 on his final Q2 lap.
Inspection of his damaged car uncovered a problem with the gearbox so the team has decided to change it for a new unit.
It means Perez will slip to 19th on the grid.
"I was trying to improve on my final lap, but I couldn't find any grip at all," said Perez of the accident.
"The crash looked far worse than it was."