Despite his crash, Albon still clocked the ninth-fastest time but his participation in the qualifying session later in the afternoon depends on whether his mechanics can rebuild his auto in time.
In a nail-biting session, Bottas saw off the five-time world champion by just 0.023 seconds at the Shanghai International Circuit.
Bottas clocked a leading time of one minute 32.830 seconds, 0.392 seconds ahead of Vettel and 0.418 of Leclerc. Ferrari's Sebastian Vettel qualified third, ahead of 21-year-old Monegasque team mate Charles Leclerc who was unable to repeat his Bahrain Grand Prix pole of two weeks ago.
Hamilton now trails Bottas in the standings by a single point.
It was neck and neck on the second runs, but Bottas managed to improve as Hamilton slipped a little in the final sector of his run and Bottas had his first pole of 2019.
"I think we are getting more and more there, understanding maybe some things related to different tracks, which Barcelona [testing] doesn't show because it's different".
"Looking on the bright side, we had a good FP2 and our race pace looks strong so I'm optimistic about tomorrow's race". "The vehicle has the pace in it to compete at the front, we just need to find the right set-up".
Albon lost control of his auto after running wide in the final corner on his fast lap in FP3, demolishing his Toro Rosso in the process.
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No one was injured in the incident and one person was taken to a police station, the embassy said. The spokesman said that contrary to some reports in the media no shots were fired from the auto .
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Bottas said: "It has been a good weekend so far".
"In Q3 honestly during those two runs I never got the flawless lap", he said.
Hamilton said: "I kept pushing right to the end".
"Valtteri has been stellar all weekend".
"[Ferrari] are quick in the straights and there are some really long straights here so for sure they are going to be a big threat and I'm sure they are going to have good race pace as well".
British novice George Russell beat Williams team-mate Robert Kubica for the third race in a row and for the first time this season the two Williams cars will not start the race from the back row.
"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". "The gap was 0.8secs at one stage so to be as close as we were is a good job and an incredible result for the team". You can run a bit wider, it just helps you bring that entry speed into the corner, and it's something I've been doing at least for the last run before and the day before as well.