BAKU (Dispatches) - The Finn lapped 0.059s faster than teammate Lewis Hamilton, who was in the tow behind him, on the final runs in Q3 to grab top spot, with Ferrari's Sebastian Vettel three tenths down in third place.
Red Bull driver Max Verstappen only had one run in Q3 and ended up fourth, almost three tenths behind Vettel and well clear of fifth fastest Sergio Perez.
Toro Rosso's Daniil Kvyat ended up sixth ahead of McLaren driver Lando Norris.
Antonio Giovinazzi headed Alfa Romeo teammate Kimi Raikkonen in the battle for eighth place, although the Italian must serve a 10-place grid penalty for taking his third power unit control electronics of the season earlier in the weekend.
Leclerc was classified 10th in Q3 as his pace on medium-compound Pirellis before he crashed meant he made the top 10 – but he was unable to run.
Leclerc was the faster Ferrari driver in free practice and Q1, but hit the wall at the narrow Turn 8 after locking up the front-left on entry during Q2 –calling the error "stupid" over the radio.
Carlos Sainz was 11th fastest after being pushed into the drop zone by teammate Norris at the end of Q2 – missing out on a place in Q3 after lapping just 0.017s than Giovinazzi.
That put him ahead of Renault's Daniel Ricciardo, with Alex Albon 13th after clipping the wall with the right-rear of Toro Rosso late on in a Q2 session interrupted by the red flag that followed Leclerc's crash.
Kevin Magnussen was 14th after locking up and heading up the Turn 3 escape road on his final lap.