The Briton, still hunting for his first win of the season, lapped the 5.2-km long Yas Marina track in one minute, 23.633 seconds on a hot afternoon with Russell 0.220 seconds adrift.
Charles Leclerc was third for Ferrari, 0.255 seconds off Hamilton's pace, ahead of Red Bull's Sergio Perez, his rival for second in the overall standings.
Mercedes head into Sunday's floodlit finale on a high, with Russell having claimed his maiden Formula One win a week ago in Brazil.
The victory, with Hamilton second, handed the once-dominant former champions a morale-boosting first triumph of the season.
But the pecking order in Friday's opening session in Abu Dhabi is rarely indicative, with the race starting at dusk and running into the night.
The lack of representative running meant teams took the opportunity to give young guns and reserve drivers some track time.
Double world champion Max Verstappen sat out the session with the Dutchman handing his car over to Formula Two racer Liam Lawson.
American Logan Sargeant, who is set to make his Formula One debut with Williams next season provided he accumulates the required superlicense points, took over departing Canadian Nicholas Latifi's car.
Mexican IndyCar racer Pato O'Ward took over Lando Norris' McLaren.
Australian Jack Doohan at Alpine, Robert Shwartzman at Ferrari, Formula Two champion Felipe Drugovich at Aston Martin, Robert Kubica at Alfa Romeo and Pietro Fittipaldi at Haas were among eight non-regulars who ran in the session.
Lawson was fifth behind the other Red Bull of Perez ahead of Sebastian Vettel in sixth.
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.
Shwartzman was seventh in Spaniard Carlos Sainz's Ferrari ahead of Daniel Ricciardo, driving in his last race for McLaren and possibly in Formula One.
Valtteri Bottas was ninth for Alfa Romeo ahead of Williams racer Alexander Albon.
The session was largely trouble free.
Sargeant survived a tyre smoking spin while Drugovich in Lance Stroll's Aston Martin and O'Ward nearly tripped over each other.
