Verstappen has previously shown what is possible at this track as in 2018 he started 19th following a power unit change and finished fifth.
The 23-year-old, however, will have Charles Leclerc directly ahead of him at the start on Sunday after Ferrari also changed the PU in the SF21 as it is running an updated hybrid system.
After topping FP1 by two-tenths of a second to team-mate Lewis Hamilton, Bottas repeated the trick in FP2, albeit with the gap slashed to 0.044s.
The Finn's lap of one minute 33.593secs arrived early on as the 10 teams conducted their qualifying simulations before switching to longer runs later in a session that was disrupted by Antonio Giovinazzi clattering his Alfa Romeo into a wall, sparking a nine-minute red flag period.
Should qualifying be unable to be completed for whatever reason on the alternative time of Sunday morning, then the times from FP2 will set the grid.
At the moment, and it all remains hypothetical given the impact of the weather, Pierre Gasly could potentially line up third behind an all-Mercedes front row.
Gasly, though, finished the session without a front wing on his AlphaTauri after running over a kerb.
McLaren's Lando Norris was fourth quickest ahead of Alpine's Esteban Ocon, with Verstappen sixth on the timesheet, just over a second down, albeit with the new PU seemingly not pushing the system to its limit just yet.
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