The German, whose exemplary lap of 1:31.095 was a new track record, was 0.530sec faster than Bottas in qualifying and 0.568sec quicker than Hamilton, who has won an unprecedented five times previously in Shanghai and arrived in town as the favourite.
Adding to his disappointment, Bottas's pace relative to the Ferraris was much better than it had been in qualifying, when neither he nor team mate Lewis Hamilton - who finished fourth - could get near the Italian cars.
Defending champion Hamilton was at a loss to explain his own lack of performance and accepted conditions on Sunday would make his job even more hard.
MercedesAMG have dominated in China for the past 7 years for the last time a Silver Arrow auto failed to line up on the pole.
The third row will be made up of the two Red Bull cars.
Red Bull's decision to change tyres under the Safety Car in Shanghai meant Verstappen and Daniel Ricciardo were able to go onto a charge in the final stint.
BC-CAR-F1-Chinese GP, 2nd Ld-Writethru, 510 Vettel takes pole in China, and Ferrari looks like it's backAP Photo CHF133, CHF125, CHF124, CHF132, CHF128, CHF122, CHF121, CHF119Eds: Updates with Hamilton quotes.
MercedesAMG' Valtteri Bottas lines up in 3rd.
"I didn't see him until very late", said Vettel. But I think that the forecast is for quite some different temperatures, some 20º C hotter track temperature. "The auto felt okay, but I don't really have the answer for it". No driver has won the opening three rounds and not gone on to take the title. I left a little bit of room. Lewis Hamilton (Mercedes) +0,5805.
Valtteri Bottas said he felt in complete control of the Chinese Grand Prix before the Safety Car period which swung the race towards its eventual victor, Daniel Ricciardo.
F1's tight midfield battle is nearly as engrossing as the battle at the head of the field given the quality of drivers in teams like Haas-Ferrari, Renault F1, McLaren-Renault, Force India-Mercedes and Toro Rosso-Honda and how close they are to each other. On harder compound tyres, there may yet be a chance for Mercedes to get the better of Ferrari.
Magnussen, Windows, Alonso, Vandorn and Hartley failed to qualify in the top 10.
He damaged his vehicle running wide in the early laps in the opening race in Australia and then spun, losing several places and finishing sixth.