Hamilton, chasing a 10th win of the year after wrapping up the championship in Mexico last month, lapped the floodlit Yas Marina circuit in one minute 37.877 seconds in the evening session.
Vettel, who had set the pace in the afternoon with a lap of 1:39.006 and looked quick on long run pace, ended the day 0.149 slower.
"It's close and I think it will be close also tomorrow," said Vettel.
The German is set to become the first non-Mercedes driver of the last four years to finish in the top two of the championship, leading Valtteri Bottas by 22 points into the final round.
Both Hamilton and Vettel, a quadruple world champion with Red Bull, are three times winners in Abu Dhabi although Ferrari have yet to triumph there.
Red Bull were third in both sessions, with 20-year-old Dutch driver Max Verstappen taking that place in the first and Australian Daniel Ricciardo in the second.
Ferrari's Kimi Raikkonen and Mercedes' Valtteri Bottas were fourth and fifth.
Brazilian veteran Felipe Massa, preparing for his last Formula One race with Williams, was 11th fastest.
The tight battle for sixth place in the constructors' championship between Toro Rosso, Renault and Haas -- with just six points separating the three teams -- is another focus for the weekend.
Nico Hulkenberg and Carlos Sainz were ninth and 13th respectively for Renault with Toro Rosso's Pierre Gasly 15th and the two Haas drivers Kevin Magnussen and Romain Grosjean 16th and 20th.
British youngster George Russell, taking part in first practise only, was 11th fastest in Esteban Ocon's Force India and less than a second off the pace of the team's Mexican driver Sergio Perez.
Russell also took part in first practise in Brazil, and looks set for a reserve role in future.
With both championships wrapped up, Mercedes having clinched their fourth successive constructors' title in Texas last month, most teams used the opening session as an early test for 2018.
Some also tried out the 'halo' head protection device that will be introduced next year.
(Writing by Alan Baldwin in London; Editing by Jon Boyle and Keith Weir)
