"We thought coming into today that we would be fighting for the pole position", said Bottas, whose reigning champion team mate Lewis Hamilton qualified fourth after aborting his final flying lap. The 33-year-old, like Vettel a four-times champion, has taken an unprecedented five wins in Shanghai.
Lance Stroll in P18 led the Sauber drivers, with Charles Leclerc, who nearly crashed his vehicle when he ran wide out of the last corner before his final lap, heading Marcus Ericsson by half a second.
By scoring 12 points on Sunday, Hamilton broke the all-time record for consecutive points finishes with 28. But more pertinently he will have begun the season with a remarkable advantage.
Lewis Hamilton reveals the real reason he struggled in Chinese Grand Prix
Vettel won this race back in 2009 and he is looking to continue his tremendous start in 2018.
Bottas was third on the grid, snatched second from compatriot Kimi Raikkonen at the start and then moved ahead of Sebastian Vettel, for the effective lead fo the race, after Mercedes pulled off a superb undercut at his first and only pit stop - the fastest of the race at just 2.15 seconds.
After allowing Vettel and Ferrari to top the podium in each of the season's first two races, this is a good place for Mercedes to bounce back.
The opening sector is a tight, twisting run that demands balance and downforce but the two major straights require low drag.
With Mercedes struggling to mount a challenge - Bottas and Hamilton were evenly matched but nearly half a second down the order - the battle for P1 came down to the red-suited drivers.
Lewis Hamilton in action at the Shanghai International circuit.
"We're lacking grip. You can fall out of the window by the tyres getting too hot or being too cold".
Warmer temperatures are predicted for Sunday and Mercedes, who struggled to get the tyres in the right temperature window, hoped that could help them in the race.
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Just two laps later Verstappen passed Hamilton to claim fourth, and both Red Bulls were charging to the top spots.
Red Bull working overtime: After Daniel Ricciardo's turbo blew up during FP3, Christian Horner said Red Bull would need to "work a miracle" in order to get the engine fixed in time for qualifying. With Renault unable to supply a pre-made replacement power unit for qualifying, the team worked relentlessly to get the Australian out.
To add a further layer of intrigue, Max Verstappen and Daniel Ricciardo, just behind Mercedes and on the third row of the grid, will start on the much faster but less durable ultrasoft compound.