Bottas was fastest with a lap of 1:18.148 seconds at the Circuit de Barcelona-Catalunya, almost a second quicker than Hamilton. Sebastian Vettel was third with Ferrari, ahead of teammate Kimi Raikkonen.
"I don't get why, for example, in golf, all the great golfers design golf courses", the Briton, victor of 63 races and four World Championships, told reporters. I was feeling good.
"We've had one pole [this season] but I don't think we've had any great qualifying sessions after that", he said. We can be better.
Hamilton added that Mercedes was "open-minded" during its attempt to understand how to extract more lap time from its W09.
"It took everything we've got to take pole", the defending F1 champion said. To get a one-two in qualifying is fantastic for the team.
"Not entirely happy, but we expected Mercedes to be very strong", Vettel said. "We have been capitalising on circumstances like the outcome of the last race (in Baku), so I will take it for now but in the long term, the team can not rely on that". Hartley will, however, be ready to compete in Sunday's race.
Formula One chairman Chase Carey said on Wednesday in a Liberty Media conference call with analysts that he hoped and believed the race would happen.
A good starting position is crucial in Spain as there are not many overtaking opportunities.
On race pace, again, it looks fairly close at the front.
Bottas was second, 0.150s down, with Vettel third, 0.269s off the pace. Vettel won in Australia and Bahrain, while Ricciardo was first in China and Hamilton triumphed in Azerbaijan. Bottas qualified second, 0.040 seconds adrift of Hamilton.
Most teams brought significant updates to Barcelona, which marks the beginning of the European season in F1. Renault's Carlos Sainz finished ninth ahead of Haas' Romain Grosjean. "So that's a positive thing".
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Renault's Nico Hulkenberg was outqualified by his team-mate Sainz for the first time this year.
The Ferrari team ran with a package of upgraded new parts on their cars including rear-view mirrors set on their "halo" head protectors.
Hartley touched the grass on the entry to the fast right-hand Turn 9 and flew sideways across the gravel into the barriers on the outside.
Carlos Sainz also cleared Alonso in the dying minutes of the session as Renault looks to recover from a hard Friday.
Q2 was all about strategy for the front-runners as the majority set their fastest times on the soft compound to ensure they start on that tire.
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