The Finn, keeping up the momentum after winning in Austria, produced a best lap of one minute 28.496 seconds - significantly quicker than Hamilton’s 2016 pole position time of 1:29.287.
Triple champion Hamilton, who bounced over kerbs and grass in the afternoon, was 0.078 behind in the morning and 0.047 off Bottas’s pace on a cloudy, gusty day when the Briton was on slower tyres than the Finn.
However, Hamilton’s chances of starting on pole position were boosted later last night when Mercedes said Bottas would collect a five-place grid penalty for a gearbox change.
Hamilton had a similar problem at the previous round in Austria which Bottas won after qualifying on pole.
“His gearbox was damaged in the same way as Lewis’ but less severely, and we had hoped to coax it to the end of the cycle,” said a Mercedes spokesman. “However, we have not been able to do so.
“The cause of the damage is understood and now behind us, just as for Lewis’ problem.”
Ferrari, more than a second slower than Bottas in the opening session, ended the afternoon as Mercedes’ closest rivals with Kimi Raikkonen third - and with a spin into the gravel - and championship leader Sebastian Vettel fourth.
“It was a bit of a mixed day, a bit up and down,” said Vettel.
“I don’t really know. We haven’t seen much yet. Yes, the new engine will help... but - well, it’s fun to drive around here!”
Hamilton, who will be chasing his fifth British Grand Prix victory and fourth in a row tomorrow, is 20 points adrift of Vettel after nine of 20 races.
Red Bull’s Dutch teenager Max Verstappen, who has had five retirements in the last seven races, was third and fourth respectively in the sessions while Australian Daniel Ricciardo was fourth and sixth.
“Mercedes look really strong but we look to be in the fight with Ferrari. At the moment we’re battling Ferrari and not Mercedes,” Ricciardo, who has been on podium for five races in a row, said after the first session.
Vettel started the morning by trying out the new “shield”, the first driver to experience the transparent open canopy system designed to protect the head from flying debris and bouncing wheels.
Governing body FIA has been focusing on that concept rather than a “halo” cockpit protection system that was extensively tested last season to a mixed response from teams and drivers.
“It’s agreed to put it on the car for next year. It is a really accelerated programme as the decision was taken a couple of months ago,” Williams technical head Paddy Lowe told Sky Sports television.
“We’re very interested to hear the feedback from Sebastian, especially on visibility. I thought it looked pretty good.
“We’re worried about reflections but there may be solutions to that. We will be testing it on various cars over the coming months.”