The Bahrain Grand Prix victor used his last lap in the dying moments of the hour-long FP3 session to bolt to a 1m29.735s and snatch top spot away from the defending champion.
Leclerc nicked the spoils by just 0.033s as Perez was only another six hundredths further back as preparations continued for a race that will now go ahead following the four-hour driver meeting on Friday night.
These crunch talks arrived after the Houthi rebels claimed responsibility for a missile attack on a nearby Aramco oil facility during FP1.
Keeping to form in 2022, it was the Alfa Romeos that wasted no time in hitting the track as Valtteri Bottas led teammate Zhou Guanyu out of the pits in FP3.
They were followed by the Haas of Kevin Magnussen, but it was a subdued opening quarter of an hour as most team plans involved installation out- and in-laps rather than a complete run.
That left the track vacant for the two Ferraris, who missed out on a combined 45 minutes of running in FP2 after both drivers tagged the wall before their medium-tyre long runs.
Leclerc and Carlos Sainz chopped and changed at the top of the times as they each completed a push lap, Leclerc posting the initial 1m31.052s benchmark on soft C4 tyres.
Sainz found four hundredths as he ran over the line after 11 minutes had elapsed to nick top spot thanks to his quicker first sector, before Leclerc dropped down to a 1m30.139s flier.
Bottas joined the Scuderia duo on track but was at first 1.4s in arrears while Sainz slipped half a second behind his stablemate, Leclerc having set the pace in both Friday practice sessions.
It took until almost 20 minutes had passed in the early evening run for the track to come alive as Lando Norris, the Williams pair and Zhou took to the asphalt.
Red Bull began its session with Perez, who ran to fourth at his first attempt while Verstappen did not emerge for a full 24 minutes as the entire field ran with C4 soft tyres.
Perez could improve to second, sitting 0.152s off Leclerc to split the Ferraris courtesy of the fastest second sector at that point while Verstappen followed a cautious prep lap with fourth.
But next time around, the Dutch racer lit up the timing screens with the fastest second and third sectors as the cooler conditions suited the RB18 and he dipped into the 1m29s.
For the first time this weekend, the 1m30s barrier was broken when Verstappen posted a 1m29.768s to run four tenths quicker than Leclerc and a strong third for Pierre Gasly.
But the AlphaTauri driver’s session was quickly hurt when he came to a stop in the pit exit with reports of a driveshaft issue with 25 minutes to run.
The pitlane was closed to avoid a red flag as the car was pushed back to the garage, from which it did not reemerge.
Verstappen might have walked away with first place when he did his heavy lifting at the halfway stage of FP3 – clocking a 1m29.768s to shoot to the head of the times.
He could have improved again in the final 10 minutes, only to abort the Turn 17 right-hand curve to clatter over the inside kerb.
That forced his RB18 to skip its front axle into the air and risk damage to the floor, following which Verstappen returned to the pits although he would remain faster than Perez.
Sainz, meanwhile, ran to fourth place, the better part of three tenths behind his stablemate, as Bottas ran to fifth ahead of Esteban Ocon and Gasly’s long-standing effort.
Magnussen kept Fernando Alonso at bay as Yuki Tsunoda completed the top 10.
Despite cutting the long-run pace deficit to the Red Bulls in half since Bahrain, the Mercedes attack could only manage 11th on the same tyre compound as Lewis Hamilton set a 1m30.707s to finish 0.9s off the pace.
George Russell, meanwhile, was 14th behind Mick Schumacher and Zhou.
As per Bahrain, it was the Mercedes-powered historic British marques bringing up the rear as Lance Stroll led an Aston Martin-McLaren-Williams train.
Behind Norris, Nicholas Latifi ran slowest and 2.2s off the pace after clipping the wall.