Perez topped the timesheets with a 1m24.982s, 0.152s clear of two-time world champion Verstappen, who could have gone quicker without a scrappy exit from Turn 5.
Hamilton ended up third-fastest and 0.240s down on Verstappen, with his Mercedes teammate George Russell a further two-tenths back in fourth.
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But Hamilton faces a post-session investigation that could see him slapped with a grid penalty.
The seven-time world champion overtook McLaren’s Lando Norris and a Haas on approach to Turn 5 just as the red flags had come out after Pierre Gasly’s AlphaTauri lost his front-right wheel deflector.
Verstappen avoided punishment for a similar incident during FP2 in Zandvoort last year but was hit with a grid drop for failing to slow under yellow flag conditions in Qatar later that season.
Norris was half a second off the pace in fifth, ahead of the Ferrari pair of Charles Leclerc and Carlos Sainz.
Daniel Ricciardo, Sebastian Vettel and Alex Albon completed the rest of the top 10 for McLaren, Aston Martin and Williams respectively.
Qualifying for the Abu Dhabi Grand Prix gets underway at 2pm UK time.