The Ferrari driver had been adrift of teammate Carlos Sainz in the early part of Q3, but on his final flying lap turned in a rapid first two sectors to steal a march on all his rivals.
A weekend-best time of 1m41.359s at Baku, a circuit thought to favour Red Bull, gave him a substantial 0.282s cushion over Sergio Perez as points leader Max Verstappen snared third.
Sainz, meanwhile, backed off on his last attempt to settle in fourth but was still some nine tenths quicker than the next car, George Russell in the Mercedes W13.
Former championship leader Leclerc, who has not won a race since the third round in Australia, was 0.05s adrift of Sainz after the first batch of quick laps in the final shootout for pole.
But he still retained second as Perez brushed the inside wall when entering Turn 5, having already oversteered on the exit of Turn 1, to nick third ahead of Verstappen.
The Ferraris were doing the damage in the first two sectors although the RB18s were faster by 0.2s on the long sprint to the line.
Sainz was first to go for a final flying lap but was slow through the Turn 5-6 chicane and messy on the exit of Turn 7 to back out of his effort.
That threw the attention on Leclerc, who set the fastest first and second sectors of the day to have a massive half-second cushion ahead of the flat-chat run to the line.
Perez was able to use the grunt of the rebadged Honda power unit to close a little after setting two personal best sectors but failed to match the rapid Monegasque across the line by nigh on 0.3s.
This came after the Mexican was late out for his final lap when the engine struggled to fire, which teammate Verstappen questioned – seemingly having been left without a tow.
The trend of Verstappen falling fractionally behind his Monaco-winning stablemate continued as the defending champion ran to a 1m41.706s, missing Perez by 0.06s.
Sainz held in fourth ahead of Russell, while Pierre Gasly ran to sixth as part of an impressive double Q3 appearance for
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