Earlier, the session was temporarily suspended after Sergio Perez clouted the wall at Turn 21.
Perez damaged his right-rear wheel in the accident before limping back to the pits.
The running was red-flagged as marshals retrieved on-track debris from the Mexican's Racing Point.
Ferrari were off the pace of Mercedes and Red Bull here on Friday, but Leclerc's quick lap suggests they could be in the fight for pole position later.
The Monegasque, 21, winner of the last two races in Belgium and Italy, saw off Hamilton by 0.207 sec.
Hamilton, who holds a 63-point championship lead over Bottas with seven rounds remaining, spun moments after he exited the pits, and later encountered traffic on his speedy run.
Alex Albon finished fifth ahead of team-mate Max Verstappen. The Red Bull pair were one second slower than Leclerc.