Vettel had won the first two races of the season, after also finishing first in the last two of 2010, from pole position and looked the favourite again after grabbing the top slot.
His team's decision to go for a two-stop strategy, rather than Hamilton's three, proved crucial with the McLaren man making the most of his fresher tyres to reel in the Red Bull after his final stop.
"The pace was there," said Vettel, who had lost out to both the McLarens at the start.
"It was there all weekend but once we decided to go to two stop you have to be patient, look after your tyres and when it doesn't work, it doesn't work.
"I saw there were seven laps to go and not much I could do.
"I don't see second today as a disappointment ... all in all we are happy with second. First was not meant to be," he added.
Red Bull's Sebastian Vettel celebrates after the Chinese Formula One Grand Prix at the Shanghai International Circuit
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