Red Bull's Max Verstappen finished fifth.
Ferrari arrived in China as favourites after looking dominant in Bahrain, a race they would have won but for a late engine problem that hit Charles Leclerc's auto while leading, and with plenty of straight line speed.
Hamilton now trails Bottas in the standings by a single point.
Hamilton added that he was "proud" of his improvements but conceded that team-mate Bottas was fully deserving of pole position.
Vettel has had the edge on Leclerc in China so far but the Monegasque came agonisingly close to beating him for the second weekend in a row.
"The lap was OK, not completely how I wanted".
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The Mercedes drivers were at the head of the line as all the teams went out at the very last minute trying to get the best track conditions.
McLaren did not enjoy a good session with Carlos Sainz and Lando Norris out in Q2 in 14 and 15.
In this photo provided by Cheung Yuk Ling, Toro Rosso driver Alexander Albon of Thailand crashes his auto during the third practice session for the Chinese Formula One Grand Prix at the Shanghai International Circuit in Shanghai, China, Saturday, April 13, 2019. It makes racing unpredictable and I'm sure we will see an exciting race tomorrow as well. More angry and disappointed than anything else. "It was a big crash, but it was a silly one as well". We had a good chance of being in Q3. "The auto has the pace in it to compete at the front, we just need to find the right set-up".
The Finn had been strong through practice and ended ahead of his Mercedes team-mate by 0.023 seconds.
Albon, who races under the Thai flag, wrote off his Toro Rosso following a 130mph shunt on the exit of the final corner in practice on Saturday morning.
"The lap was ok, not completely how I wanted it but it was good enough for pole and the auto has been good enough this weekend and Lewis has improved today too".
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"The Ferrari really squeezed it out at the end and I'm happy". Big congratulations to Valtteri.
"I'm quite proud of job I've done considering how far I was off. Valtteri has been quick all weekend". I have been struggling and chipping away at it.
Vettel, whose contract with Ferrari ends in after the 2020 season, also responded to suggestions made by F1's former chief executive, Bernie Ecclestone, that the German might quit the sport. "We had a good session".
"It's nice to be on pole - I haven't had that many of those in my career", said the world championship leader after taking top spot in qualifying for the seventh time.
Ferrari had arrived in China as favorites after showing their speed in Bahrain, particularly on the straights, with Leclerc on pole and leading until a loss of engine power in the closing laps. "Today was a good day and hopefully tomorrow will be again".
To mark the 1,000th race, several drivers have changed their helmet designs.
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As well, the government plans to make changes to the way it funds the province's 45 publicly assisted post-secondary institutions. And the Tories intend to move forward with a previously announced plan to put beer and wine in corner stores.