Bottas had topped the morning session and was a second faster than the Dutchman on the early medium-tyre runs, but was unable to improve on his soft-tyre run.
Mercedes, however, will be content with the performance shown on a 'normal' track layout after struggling on the Monaco and Azerbaijan street circuits.
The track temperature peaked at 48.3 degrees centigrade but was paired with the high 'Mistral' wind, which lends its name to the long back straight at Paul Ricard, which made conditions tricky for the drivers.
Bottas was the first of the frontrunners to switch to the soft tyres but the high temperatures clearly affected his grip in the final sector, ending slower than his lap on the medium tyres.
As the temperatures cooled, however, Verstappen was able to hook up both the first and last sectors to edge ahead of Bottas with a one minute 32.872secs.
Hamilton was two-tenths adrift having complained that there was "something not right with the car" during his qualifying simulation.
Verstappen's running was interrupted early on as he fell foul of the aggressive kerbs lining the exit of turn two, losing part of his front wing early in the session.
Unlike Mercedes, who sent a combative message to the FIA when Bottas damaged his car over the kerbs in FP1, Red Bull sporting director Jonathan Wheatley said: "We are a bit short on those bits of carbon, it would be good if we could have it back."
Race director Michael Masi responded: "No problem, we will get that back to you at the end of the session."
However, at the end of the session, the team complained that the penalty was too harsh in terms of damage for running not too far wide, effectively echoing Mercedes' gripes.
Fernando Alonso impressed to finish 0.468secs away from Verstappen in fourth, with team-mate Esteban Ocon, fresh from signing a new three-year deal with Alpine, sandwiching Ferrari's Charles Leclerc.
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