While Bottas lapped in one minute 34.923 seconds, Hamilton was only 19th and 2.7 seconds slower than the Finn in a session that saw McLaren's Carlos Sainz and Williams' Nicholas Latifi crash and others spin. It was the sixth time in a row that Bottas, who has so far won only the opening race in Austria in July, had been fastest in first practice.
Mercedes technical director James Allison told Sky Sports television that Hamilton had damaged his hard tyres early on in the session and then focused mainly on data gathering. "It's incredibly easy to lock up a tyre and destroy the tyre set for the remainder of the session," he said. "We fell foul of that with both our drivers today, not really getting anything out of the medium and hard tyres.
"Lewis to boot had a tough time on his soft run as well, again making that mistake of locking the tyres up and then the run being done. Not a great session for us by any means," said the Briton. The Russian Grand Prix will be the first race of a COVID-hit season with a significant number of fans present.
Mercedes have won every race at the Sochi circuit since the first in 2014, with six times world champion Hamilton triumphant on four occasions. The champions have also started every race this season on pole position.
Hamilton leads Bottas, who set his fastest lap on soft tyres before damaging his set of mediums, by 55 points after nine races. Australian Daniel Ricciardo was second fastest for Renault, 0.507 off Bottas's pace, with Red Bull's Max Verstappen third fastest and 0.147 further back. Sainz's crash, with the McLaren suffering a broken rear wing after hitting the barriers, brought out a virtual safety car while Latifi triggered a red flag when he went into the tyre wall.
Mexican Sergio Perez was fourth fastest for Racing Point with Canadian team mate Lance Stroll fifth and Renault's Esteban Ocon sixth. Sebastian Vettel was the highest Ferrari driver in ninth with team mate Charles Leclerc, on pole last year in Russia, 11th.