The Monegasque lapped a dusty Hungaroring track in 01:19.075 seconds before ending his session with seven minutes to spare after telling the team that 'something broke' on the car.
Red Bull's Max Verstappen was second on the timesheets, 0.484 slower and facing a trip to the stewards for allegedly driving erratically, with Ferrari's Lewis Hamilton 0.543 off his teammate's pace in third.
Hamilton was unhappy with his car's handling, saying over the radio that it felt "pretty bad. Ride is very poor. The stiffness is too stiff."
Mercedes' championship leader Kimi Antonelli sat out the session, with Danish reserve Frederik Vesti given time in the car and lapping seventh fastest. George Russell was fifth, 0.991 slower than Leclerc.
McLaren's world champion Lando Norris was 11th, with last year's Formula Two champion Leonardo Fornaroli taking Oscar Piastri's car and ending up 16th.
The session was briefly halted after Lance Stroll spun off in the upgraded Aston Martin, which is effectively a new car, such is the extent of the changes.
Teammate Fernando Alonso was 13th fastest with a time 2.475 seconds slower than Leclerc, which gives Aston real hope that their updates have led to significant improvement.
Despite Ferrari's strong start to the Hungarian weekend, after winning two of the previous four races, Leclerc and Hamilton both warned that Mercedes were still the clear favourites even if the track was more to Ferrari's liking than recent ones.
"I still personally expect Mercedes to be the reference and they are going to be very difficult to beat on the qualifying lap," said Leclerc.
"I think Mercedes are still the team to beat," eight-time Hungarian GP winner Hamilton said on Thursday.