He let Bottas get briefly ahead during the initial runs in Q3, after locking up and running wide at Turn 16 on his quickest lap, before Daniel Ricciardo's Red Bull hit the wall at Turn 6, bringing out the red flags and spoiling a potentially faster lap for Hamilton.
But for Vettel, who heads Hamilton in the title race by 12 points heading into the eighth round of the season, his morning was plagued by a technical problem.
Force India followed up on its promising practice pace with sixth and seventh on the grid ahead of the two Williams of Lance Stroll and Felipe Massa. "It's not about being greedy, it's about having that right balance; it's basically like a see-saw and I had a ideal balance between aggressiveness and taking too much out".
"That was one of the most exciting laps I've had all year and a lot of pressure", Hamilton said. It was the first time we tried to go for a time in the first lap of the tyres and I couldn't get them to work as well as Lewis. "A lot of pressure".
Though he improved his time in the burst of 3 minutes and 33 seconds that remained, he was undone by Hamilton's stunning lap to trail by 0.434 seconds.
"So to come in this morning not really knowing if those changes were going to be right, I know I've got full confidence with the team but still it's very hard with the tyres to switch them on and off. All weekend we've struggled to switch the auto on over a single lap, but it was an all or nothing moment so I just gave it everything I had".
Accepting responsibility for his qualifying result, Vettel said, "In the end, I was alone and had no tow in the last sector". The vehicle was very good yesterday and in the long run we looked very competitive.
"I'm no fan of excuses, I could have done a bit better but probably P3 was the maximum".
Nico Hulkenberg was 11th, while his Renault teammate Jolyon Palmer failed to set a representative time after stopping on track early on with a fire at the rear of the vehicle. That will promote Kevin Magnussen up to 12th, Nico Hulkenberg to 13th and Pascal Wehrlein to 14th after another impressive performance from the Sauber driver.