Hamilton posted a lap of one minute 26.621secs around Silverstone, beating Bottas by 0.163s as Mercedes scored its third consecutive one-two across practice, with the six-time F1 champion taking the head-to-head two-one over the Finn.
That has set up another qualifying showdown between the two as it appears odds-on it will be another front-row lock-out for the race.
For the first 40 minutes of the hour-long session, Hamilton and Bottas traded places on a few occasions before McLaren's Lando Norris set the fastest time with a lap of 1:27.202s, and on the medium-compound tyre.
Normal order was soon restored, though, as Norris' time was usurped by Bottas by four-tenths of a second on the softs, with Hamilton then claiming what proved to be the best lap of the session a couple of minutes later.
Norris' time was good enough for third quickest on the timesheet, followed by Racing Point reserve Nico Hülkenberg who finished just over six-tenths of a second down on Hamilton, and seven-thousandths ahead of team-mate Lance Stroll.
Following the engine failure on Sebastian Vettel's car in the closing minutes of FP2, Ferrari opted to replace the internal combustion engine, traction control and MGU-H in the German's SF1000.
As a safeguard, with an investigation to take place at Maranello over the coming days, the team also replaced the same parts in the power unit of Charles Leclerc's car.
That allowed Leclerc to set the sixth-best lap, albeit seven-tenths of a second down on Hamilton, while Vettel again struggled as he was a lowly 13th, 1.190s adrift.
Following Friday practice, a concern for all the teams was the rapid degradation of the soft tyre, in particular given the hot conditions across Silverstone this weekend.
Pirelli is running a step softer across the three compounds, a move boss Mario Isola confirmed on Friday was at the request of F1 and the FIA to improve the show in the second of the back-to-back races at the Northamptonshire circuit.
All teams have determined the soft tyre will not be the one on which to start the race, so Q2 will see the 15 drivers involved seeking to avoid running that rubber to get into the top 10.
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