For the fifth time in 10 practice sessions at the futuristic track, Hamilton set the pace as he spearheaded a McLaren one-two, finishing exactly a third of a second quicker than Jenson Button.
Hamilton's lap for the 5.554-kilometre track of one minute 43.285 seconds was also set on the harder of the two Pirelli compounds for this weekend, the medium, with the quicker soft rubber being saved for session two.
Over the three years the race has been staged in Abu Dhabi, Hamilton and Sebastian Vettel have locked out the front row of the grid between them - the latter claiming two poles to the former's one.
After the opening 90 minutes today Vettel was forced to settle for the third-quickest time, with the 25-year-old German finishing 0.765secs behind Hamilton, with everybody else over a second down.
That included Ferrari's Fernando Alonso, the only driver who can realistically stop Vettel from making it three titles in a row as the duo go into the last three races separated by 13 points.
With Ferrari experimenting with new parts, Alonso was fourth, a fraction over a second off Hamilton's pace, and a quarter of a second behind Vettel.
Red Bull's Mark Webber was the best of the rest, followed by Michael Schumacher in his Mercedes and Williams' Pastor Maldonado.
For a long period towards the end of the session the Venezuelan and reserve driver Valtteri Bottas were locked on exactly the same time until the former put in a lap two-tenths of a second quicker.
That left Bottas, tipped to take over from Bruno Senna at Williams next season, ninth on the timesheet, two seconds behind Hamilton and just behind Nico Rosberg in his Mercedes.
Lotus' Kimi Raikkonen, who this week signed a new one-year contract with the Enstone-based marque, was 10th and 2.137secs adrift, with Felipe Massa in his Ferrari 11th, 1.2secs behind team-mate Alonso.
Force India's Nico Hulkenberg, bound for Sauber next season, was 12th and 0.182secs ahead of reserve Jules Bianchi as Paul Di Resta stood aside for the session.
On his Formula One debut as Marussia reserve, 21-year-old Max Chilton acquitted himself well, completing 22 laps, with his best 5.602secs down on Hamilton.
More pertinently, and as a greater judge, Chilton was a second behind team-mate Timo Glock, although in running specific programmes it is hard to assess the merit of his time on the whole.
Two other reserves in HRT's Ma Qing Hua and Caterham's Giedo van der Garde sat at the bottom of the standings, the latter failing to set a time and only completing three installation laps due to an issue with his car.