Super stand-in Nico Hulkenberg qualified his Racing Point an eye-opening third as a replacement for absent Mexican Sergio Perez, in quarantine after testing positive for COVID-19.
Red Bull's Max Verstappen joined the experienced German on the second row.
The front row lockout was a record-extending 67th for Mercedes and switched around last weekend's British Grand Prix qualifying, where Hamilton took his 91st career pole and won despite a last-lap puncture while Bottas failed to score.
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"Things are going to be a bit different to last weekend in terms of strategy," said Bottas, who lapped a mere 0.063 quicker than Hamilton.
The Briton congratulated the Finn on his 13th pole, which ended his own run of three in a row.
"Valtteri did a good job and deserved the pole. For me, it wasn't a perfect last lap," said the six times world champion, who leads his team mate by 30 points after four races.
Australian Daniel Ricciardo qualified fifth for Renault, with Canadian Lance Stroll sixth for Racing Point.
Charles Leclerc was the highest-placed Ferrari driver in eighth, with his four-times world champion team mate Sebastian Vettel failing to make the top 10 session and qualifying only 12th.
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