Red Bull driver Verstappen provided the filling in a Mercedes sandwich as Lewis Hamilton was 0.123s behind team-mate Bottas' leading time of one 1:18.504s at Barcelona's Circuit de Catalunya.
There was a major scare for Bottas towards the end of the hour-long session as he came close to running into the back of Ferrari's Carlos Sainz on the approach to the chicane.
The Finn was forced to head off track to avoid a collision with the Spaniard as traffic built up over the closing stages due to several minutes of lost running after Alfa Romeo reserve Robert Kubica beached his car in a gravel trap at the reprofiled turn 10.
Following an early run on the soft tyres from Fernando Alonso in his Alpine that sent him to the top of the timesheet, Hamilton quickly topped that on the hard compound by two-tenths of a second.
Sporting the revised floor that was on the car of team-mate Lance Stroll in Portugal, Aston Martin's Sebastian Vettel leapfrogged Hamilton on his own soft-tyre session by just over four-tenths.
The seven-time F1 champion, however, soon switched to Pirelli's red-banded rubber, reclaiming his place at the head of the field before ultimately losing out to Bottas.
In the closing stages, Verstappen managed to split the Mercedes pair, that after his running had been earlier compromised when he ran over the high kerb at the exit of turn seven.
That necessitated a return to the garage for a damage check to the front wing and floor and cost the Dutch driver 15 minutes of track time.
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