Red Bull's Max Verstappen will start the Italian Grand Prix from the back of the grid.
Leclerc defeated Verstappen by 0.145 seconds.
Nine drivers have a grid penalty, and Verstappen is one of them.
McLaren's Carlos Sainz, Red Bull's Sergio Perez, and Mercedes' Lewis Hamilton were the top five.
George Russell is likely to start second on the grid.
The winner of this race, Leclerc, said it was amazing. The session wasn't easy. I knew there was a lot of potential in the car but I didn't put it all together until the last lap.
The car feels great and I hope I can finish it tomorrow.
Verstappen, who is on course to win a second title within two or three races, said: "The lap was pretty decent just the first sector."
The races runs felt good and I am looking forward to the race.
Lando was eighth fastest, ahead of Daniel, who was the Australian's best performance since the Emilia Romagna Grand Prix.
Pierre Gasly qualified ninth, ahead of Fernando Alonso.
Alonso's second lap was deleted after he exceeded track limits at the second Lesmo on his final lap.
He said that the Q3 wasn't very well executed. The first run was not great. I apologize for not putting a lap together. The lap I put together was only good enough for P8 so it seems we are lacking a bit of performance in the event. We can improve tomorrow.
It is difficult to work out the grid order due to the many penalties.
Nick de Vries is probably going to be promoted into the top 10 in the Williams.
After Alex Albon was diagnosed withAppendicitis, De Vries was drafted in and qualified 13th.