Four-time champion Sebastian Vettel took second for Aston Martin after an impressive drive after qualifying 11th. Pierre Gasly was third for AlphaTauri.
Mercedes driver Lewis Hamilton and his Red Bull rival Max Verstappen would like to see team bosses Toto Wolff and Christian Horner don boxing gloves to settle their differences.
AlphaTauri's Gasly was fastest in a time of 1 minute, 42.251 seconds, beating Perez by .344 seconds.
Mercedes didn't challenge for the top positions, with Lewis Hamilton seventh and Valtteri Bottas 10th.
Winning the last race in Monaco put Verstappen four points ahead of Hamilton heading into the Azerbaijan Grand Prix.
Hamilton followed his 100th career pole on Saturday by taking his 98th career win. He also tied Michael Schumacher's mark of six victories at the Spanish Grand Prix.
Verstappen pushed his Red Bull to a session-best lap of 1 minute, 17.83 seconds.
On Saturday, Hamilton will be aiming for his 100th career pole. On Sunday, he will be looking to equal Michael Schumacher’s six wins in Montmeló.
At a track all teams know well, Mercedes and Red Bull are expected to continue to dominate with Lewis Hamilton and Max Verstappen separated by eight points after three races.
Max Verstappen won a dramatic Emilia-Romagna Grand Prix on Sunday after world champion Lewis Hamilton hit a wall in a race.
Mercedes led the two practice sessions on Friday with Valtteri Bottas fastest in both, just ahead of Hamilton as Red Bull endured a tough start to the weekend.
The race was effectively decided when Verstappen overtook Hamilton but went too wide on a turn and was told by his team to give Hamilton the position back, as he risked a time penalty.
Verstappen earned his fourth career pole to deny Hamilton his 99th, edging out the world champion by .39 seconds on his final attempt.
The Red Bull driver was .298 seconds ahead of Mercedes driver Valtteri Bottas and .503 clear of McLaren's Lando Norris.
He finished 16 seconds ahead of Valtteri Bottas and 18.4 clear of world champion Lewis Hamilton as Red Bull enjoyed a rare and significant success over both Mercedes cars.
He was .025 seconds ahead of Valtteri Bottas and .086 clear of world champion Lewis Hamilton for his first pole of the season and third of his career.
Verstappen led Albon by .5 seconds and Renault driver Daniel Ricciardo by .63.
The Red Bull driver was .34 seconds ahead of Mercedes rival Valtteri Bottas and 1.14 seconds quicker than Renault driver Esteban Ocon.
He moved up the leaderboard late in the session to finish .21 seconds ahead of Mercedes driver Valtteri Bottas and .36 clear of Bottas' temporary teammate George Russell.
Verstappen was .94 seconds quicker than Ferrari's Charles Leclerc and 1.57 ahead of Red Bull teammate Alexander Albon.
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