Making the most of the quicker soft tyres, Hamilton was able to put together a run of several quick laps and surprised by finding time in the final sector, traditionally Red Bullâ€™s strongest.
Vettel, who wrapped up his maiden Formula 1 world driversâ€™ title in Abu Dhabi 12 months ago, was the only driver with a chance of beating Hamiltonâ€™s benchmark, but was slower than Hamilton on the straights in sector two.
The German was then held up by traffic in the final sector of his last lap and had to settle for second, just 0.024 quicker than team-mate Mark Webber.
Such was Hamiltonâ€™s dominance through the final sector, Webber, who was quickest in the first two sectors, was 0.4s off the Britonâ€™s time just in the final sector.
Hamiltonâ€™s team-mate Jenson Button was fourth quickest in the final session, within one tenth of the Red Bulls, but seemingly unhappy with his car as the team continued to make changes through the session.
Ferrariâ€™s Fernando Alonso was fifth quickest, and the only other driver sub 1m40, but lacked grip in the final sector of the circuit and was almost seven tenths off Hamiltonâ€™s time.
Mercedesâ€™ Nico Rosberg was sixth quickest, albeit a second slower than Hamilton, just ahead of Ferrariâ€™s Felipe Massa.
Both Force India cars again made it into the top 10 as Adrian Sutil was just a tenth quicker than team-mate Paul di Resta in eighth and ninth, with Michael Schumacher rounding out the top 10 in the second Mercedes, eight tenths slower than team-mate Rosberg.
Further back, Renault struggled and will face a battle with Force India to get into the top 10 shoot-out in qualifying. Bruno Senna was 11th fastest, with Russian driver Vitaly Petrov slower than the two Saubers in 14th.
Surprisingly, Toro Rosso also struggled around the marina, managing just 15th and 16th quickest.
Heikki Kovalainen found some performance in the Lotus to lap four tenths quicker than Williamsâ€™ Rubens Barrichello, with the Brazilian sidelined for much of the session with an oil leak.
Timo Glock was almost 1.4s slower than Barrichello with a 1m45 262, ahead of HRTâ€™s Tonio Liuzzi, team-mate JÃ©rÃ´me dâ€™Ambrosio, and Daniel Ricciardo.
Kovalainenâ€™s team-mate, Jarno Trulli failed to set a time due to a gearbox problem.
MORE: The latest football news
MORE: The latest tennis news