The Lotuses of Kimi Raikkonen and Romain Grosjean set the pace early on before Hamilton went out and shot straight to the top of the leaderboard.
Vettel didn't set a hot lap until the final moments because of a brake problem but did manage to usurp teammate Webber in third with his final attempt at the Yas Marina circuit.
Vettel's world championship challenger Fernando Alonso was eighth fastest.
Qualifying for tomorrow's race takes place later this afternoon.
1. Lewis Hamilton (McLaren)
2. Jenson Button (McLaren)
3. Sebastian Vettel (Red Bull)
4. Mark Webber (Red Bull)
5. Nico Hulkenburg (Force India)
6. Romain Grosjean (Lotus Renault)
7. Pastor Maldonado (Williams)
8. Fernando Alonso (Ferrari)
9. Kimi Raikkonen (Lotus Renault)
10. Paul di Resta (Force India)
11. Felipe Massa (Ferrari)
12. Sergio Perez (Sauber)
13. Nico Rosberg (Mercedes)
14. Michael Schumacher (Mercedes)
15. Kamui Kobayashi (Sauber)
16. Jean-Eric Vergne (Toro Rosso)
17. Bruno Senna (Williams)
18. Daniel Ricciardo (Toro Rosso)
19. Heikki Kovalainen (Caterham)
20. Timo Glock (Marussia)
21. Charles Pic (Marussia)
22. Vitaly Petrov (Caterham)
23. Pedro de la Rosa (HRT)
24. Narain Karthikeyan (HRT)