George Russell set the pace with a fastest lap of 1:24.418s ahead of Lando Norris and Oscar Piastri.
Norris went second quickest and was 0.095s down on Russell on the Soft tyre, after having a big wheel spin moment exiting the final corner.
Alex Albon was fourth quickest ahead of Charles Leclerc, with the Ferrari driver setting his quickest lap in the last 10 minutes of the session.
Verstappen aborted his first attempt on the Soft tyres after struggling to find grip on his lap, but set a time in the dying moments of the session to go sixth fastest and 0.735s off the pace.
Result Free practice 3 - Abu Dhabi
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Hamilton set the initial pace on the Soft tyres after being among the first to head out to set a lap time.
He elected to not do another timed run on the Soft tyres, tumbling down to P12 behind Sergio Perez in P12.
Less than ten minutes into the session Perez managed to go quicker by 1.195s on the Softs, showing the same level of track evolution as yesterday.
Ferrari elected to use the session to focus on their race runs, with both drivers running the Medium tyre for the majority of the session before switching to the Soft tyres in the closing stages of the session.
Elsewhere Williams looked quicker than AlpahTauri over the course of a lap, with Daniel Ricciardo struggling to match teammate Yuki Tsunoda on the Soft tyres.