The German, starting from pole, fought off Nico Rosberg in the first corner and despite a safety car intervention, he was untouchable as he scored his third win in a row and a hat-trick of wins in Singapore.
Ferrari's Alonso finished second to keep up the title pressure on Vettel, who now leads the championship by 60 points from the Spaniard with six races remaining.
Lotus driver Kimi Raikkonen braved back pain to finish third but there was disaster for Red Bull's Mark Webber, whose late charge ended in a blown engine and a ride back to the pits on the wing of Alonso's Ferrari.
But yet again the race belonged to Vettel, who was literally streets ahead of his rivals on the spot-lit Marina Bay circuit through the highways of downtown Singapore.
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"The start was quite hairy, Nico had a better start and I didn't get going," said Vettel. "But unfortunately he went a little too deep and I could get it back.
"With the safety car it was difficult but as soon as the safety car came off we had very strong pace with the car. It was just a pleasure to drive around this crazy race."
From the start, Rosberg arrowed past pole-sitter Vettel going into the first turn but his speed carried him wide at the second corner and the Red Bull man was able to nip back in front.
Behind them, Alonso pulled off a masterful move as he used the outside of the track to leap from seventh on the grid to third in the opening seconds.