The drivers took to the demanding 23-turn street circuit two hours after a tropical downpour had soaked the track with Vettel, the winner here a year ago, clocking the fastest lap of 1 minute 50.566 seconds late in the session in his Red Bull.
Hamilton lapped 0.049 seconds slower than Vettel as his McLaren continued to display the pace that has carried him to two victories in the last three races. The Briton's team mate Jenson Button was third fastest, 0.893 seconds off the leader.
Championship leader Fernando Alonso was fourth fastest in his Ferrari, marginally ahead of the Williams of Pastor Maldonado, Mark Webber in the other Red Bull and Force India's Nico Hulkenberg.
The 90-minute session got off to a slow start as a majority of the 24 drivers on the circuit waited until the sun set to attempt lap times, as they sought to compete under the floodlit conditions experienced in qualifying and on raceday.
The threat of a second thunder storm towards the end of the session was relayed to the teams and although the downpour failed to materialise, the track was packed for the last 30 minutes as drivers sought to set fast times on soft tyres.
The Mercedes of Michael Schumacher and Nico Rosberg showed plenty of early speed as they tested an upgraded exhaust system but the pair fell away as the session progressed to finish 14th and 18th fastest respectively.
Former world champion Kimi Raikkonen (12th) and Sebastian Grosjean (15th) would also be disappointed with the performance of their cars, the Lotus duo lapping more than two seconds off the pace at a circuit where they are expected to do well.
The Marina Bay Circuit is regarded as one of the most challenging on the 20-race calendar but apart from several drivers missing the apex on the tricky turn 10 chicane, only two cars slid off the track into runoff areas in the entire session.
1. Sebastian Vettel (Germany) RedBull - Renault 1:50.566
2. Lewis Hamilton (Britain) McLaren 1:50.615
3. Jenson Button (Britain) McLaren 1:51.459
4. Fernando Alonso (Spain) Ferrari 1:51.525
5. Pastor Maldonado (Venezuela) Williams - Renault 1:51.576
6. Mark Webber (Australia) RedBull - Renault 1:51.655
7. Nico Huelkenberg (Germany) Force India - Mercedes 1:51.658
8. Paul Di Resta (Britain) Force India - Mercedes 1:51.943
9. Daniel Ricciardo (Australia) Toro Rosso - Ferrari 1:52.275
10. Sergio Perez (Mexico) Sauber - Ferrari 1:52.296
11. Bruno Senna (Brazil) Williams - Renault 1:52.629
12. Kimi Raikkonen (Finland) Lotus - Renault 1:52.716
13. Kamui Kobayashi (Japan) Sauber - Ferrari 1:52.839
14. Michael Schumacher (Germany) Mercedes 1:52.986
15. Romain Grosjean (France) Lotus - Renault 1:53.028
16. Felipe Massa (Brazil) Ferrari 1:53.080
17. Jean-Eric Vergne (France) Toro Rosso - Ferrari 1:53.189
18. Nico Rosberg (Germany) Mercedes 1:53.227
19. Timo Glock (Germany) Marussia - Cosworth 1:54.908
20. Heikki Kovalainen (Finland) Caterham - Renault 1:55.091
21. Charles Pic (France) Marussia - Cosworth 1:55.335
22. Vitaly Petrov (Russia) Caterham - Renault 1:55.760
23. Pedro de la Rosa (Spain) HRT - Cosworth 1:56.656
24. Ma Qinghua (China) HRT - Cosworth 1:58.053