As was the case a week ago ahead of the Belgian Grand Prix, Bottas had the edge in FP1 ahead of Mercedes team-mate Lewis Hamilton.
In the opening 90-minute session for the Italian Grand Prix, Bottas finished top of the timesheet again with a lap of one minute 20.703secs, finishing 0.245s ahead of Hamilton.
As for Verstappen, the Dutch driver brought out a rare red flag in practice this season after 35 minutes of the opening run.
The 22-year-old lost the rear of his Red Bull midway through the Ascari chicane, clipping a kerb en route that sent him into a gravel trap and into a barrier which wrenched off the front wing.
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Verstappen at least managed to keep the engine going, allowing him to expertly reverse his way out of his predicament and return to the garage where he was able to receive a new nose.
Come the conclusion, Verstappen finished fifth on the timesheet, 0.938s adrift of Bottas, with team-mate Alex Albon for once ahead of him by 0.141s.
The surprise package was AlphaTauri, with Daniil Kvyat and Pierre Gasly sixth, the duo 0.852s and 0.964s down respectively, and with both on the medium-compound tyre compared to the soft runners around them.
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