Ferrari teammate Kimi Raikkonen was second and will start next to Vettel on Sunday.
Bottas beat Hamilton with the top three of Vettel-Raikkonen-Bottas a repeat of the outcome in Bahrain qualifying a week ago. But in a repeat of the dramatic conclusion to qualifying in Bahrain a week ago, Vettel produced a stellar last-gasp effort to claim pole by less than a tenth of a second.
The Prancing Horse replicated their advantage, with Raikkonen and Vettel setting an impressive pace on the more durable rubber. Mercedes are now under real pressure. The 33-year-old, like Vettel a four-times champion, has taken an unprecedented five wins in Shanghai.
Formula 1 World Championship leader Sebastian Vettel will start from Pole Position for tomorrow's Chinese Grand Prix.
And with Valtteri Bottas finishing second, it means for the first time in the V6 era, Mercedes have failed to win for three successive races. They were so fast on fresh tyres.
For Hamilton, pictured, already 17 points behind Vettel, he will line up only fourth following a disappointing day in the gloom of Shanghai.
Hamilton appeared to be struggling with understeer and a lack of grip and bringing the tyres up to temperature throughout the session. The only time he was faster than the Finnish driver was when Bottas crashed out of Q3 at the Australian Grand Prix.
Mr. Hamilton struggled for pace Saturday, spinning during the morning practice session, before qualifying behind Mr. Bottas for the 2nd time in 2 races.
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Red Bull Racing's drivers set only one lap each on the ultrasoft tyres, which left them vulnerable to improvements from the midfield drivers on the final runs.
Ricciardo emerged with just two minutes left of Q1 after another Renault engine failure on the Australian's vehicle during Practice Three.
RBR principal Christian Horner said his team would need a miracle to get the auto out in time to qualify, but with three minutes left on the clock Ricciardo left the pit lane to set one flying lap.
Daniel Ricciardo was the surprise victor of the Chinese Grand Prix as inspired tactics by his Red Bull Racing team and some ruthless overtaking gave the Australian victory in Shanghai.
The rest of the top ten sees Hulkenberg in the Renault in seventh, the Force India of Perez in eighth, the second Renault driven by Sainz in ninth and Romain Grosjean for Haas in 10th. The McLaren twins piloted by Fernando Alonso and Stoffel Vandoorne were up next in 13th and 14th place respectively after being eliminated on Q2.