Lotus-Renault driver Kimi Raikkonen of Finland takes the first turn during the qualifying session of Formula One's Chinese Grand Prix at the Shanghai International Circuit. AFP/Mark Ralston
Alonso, who is 29 points clear of Vettel with six races to go, will start on the third row in sixth place, while Japan's Kamui Kobayashi in a Sauber delighted the home crowd by taking third.
Vettel and Alonso were both called to the stewards afterwards, however, with the German accused of impeding the Spaniard at the last corner in the dying seconds.
Vettel's lap of one minute 30.839 denied title rivals McLaren, whose drivers were off the pace anyway, a fifth pole in a row for the season.
Jenson Button was demoted five places for a gearbox change to eighth while McLaren team mate Hamilton will start ninth. Frenchman Romain Grosjean (Lotus) will line up in fourth ahead of Mexico's Sergio Perez (Sauber) in fifth.
Vettel's 34th career pole lifted the 25-year-old to third in the all-time list behind seven-times champion and compatriot Michael Schumacher (68) and the late Brazilian Ayrton Senna (65).
"We had a very smooth qualifying session, nearly perfect," said Vettel, who has won two of the last three races at the figure-of-eight circuit overlooked by the giant fairground Ferris wheel.
"I couldn't really ask for more. The car felt fantastic from the start."
Alonso upset
Alonso was left cursing his luck Saturday after Raikkonen’s late spin.
"What can I say, other than get angry about being unlucky? The yellow flags came at the worst possible moment, when I was coming into turn 14," Alonso said.
"Up until then, my lap was great and there was every chance of setting the fourth fastest time of the day, which would have then seen me start from third on the grid.”