The Dutchman, who had handed his car to Red Bull reserve Liam Lawson (20) during Friday afternoon's opening hour of running, lapped the 5.2-km long Yas Marina track in one minute 25.146 seconds.
George Russell (24), who took his maiden Formula One win ahead of teammate Lewis Hamilton (37) in a Mercedes one-two last week in Brazil, was second 0.341 seconds adrift, with Ferrari's Charles Leclerc (25) third.
Verstappen, who wrapped up a second title with four races to spare at the Japanese Grand Prix last month, heads into the weekend hunting for a record-extending 15th victory of the season at the track where he clinched his first title with a controversial win last year.
Hamilton, in his resurgent Mercedes meanwhile, is hunting for his first triumph of the year, with Sunday's race his last chance to keep his record of winning a grand prix in every season intact.
The Briton had led the opening hour of practice in a Mercedes one-two from Russell but fell to fourth under the floodlights, 0.615 seconds off Verstappen's pace.
Mexican Sergio Perez (32), level on points with Ferrari's Leclerc in their battle for second in the overall standings, was fifth in his Red Bull ahead of Ferrari's Carlos Sainz (28).
Frenchman Esteban Ocon (26) led Alpine teammate Fernando Alonso (41) in seventh with McLaren's Daniel Ricciardo (33) and Alfa Romeo's Valtteri Bottas (33) rounding out the top 10.
Sebastian Vettel (35) ended his final session of Friday practice in 12th for Aston Martin.
The four-time champion is calling time on his career after Sunday's race and TV pictures captured an emotional moment between the German and his father ahead of the session in the Aston Martin garage, which was decked out with a photo cutout of a young Vettel and his karting overalls.