In Friday practice at Monza, Bottas was quickest in FP1, with Hamilton reversing the order for FP2, but come the final 60-minute run it was the Finn who held sway.
Bottas posted a time of one minute 20.089secs, which looked highly marginal for exceeding track limits upon exiting the Parabolica, but it was allowed to stand by the stewards.
The lap was posted with 15 minutes of the session remaining and stood through to the conclusion as no-one came close, with McLaren pair Carlos Sainz and Lando Norris finishing second and third quickest, finishing 0.229s and 0.323s adrift.
With nine minutes of the session remaining, Daniel Ricciardo suffered a suspected fuel pump failure, pulling his Renault over on to the grass at Lesmo just after he had posted the third quickest lap at that time.
Race director Michael Masi was forced to red flag the session while Ricciardo's R.S.20 was removed given it was parked in a dangerous position.
Given the timing of the stoppage, it naturally ruined the qualifying simulation runs of many drivers at the time, leading to a stampede out of the garages when the session resumed with three minutes and 30 seconds remaining.
The late rush to the track ultimately played a major role in Hamilton's incident, with the Briton finishing fifth quickest, 0.350s behind Bottas.
Ricciardo ultimately finished fourth fastest, and should be ready to go for qualifying as the fuel pump is a replaceable part according to Renault.
Red Bull pair Max Verstappen and Alex Albon were sixth and seventh on the timesheet, albeit with the Dutch driver on the medium tyre.
It proved to be a fascinating session, not least because the FIA had issued a note to the teams clarifying that drivers must remain below a time of one minute 43 seconds for an out lap prior to setting a hot lap.
This was done after assessing lap times across Friday's sessions, and in order to avoid the farce that unfolded in last year's qualifying and ahead of F3 qualifying on Friday, which left Daniel Ricciardo in a rage.
The notes read: "For reasons of safety, during each practice session, acts such as weaving across the track to hinder another car may be referred to the stewards,” read the notes.
“During FP3 and qualifying, the time published will be used as a guide by the stewards to determine if a driver is considered to be driving unnecessarily slowly on an out lap or any other lap that is not a fast lap or in lap.”
Yet throughout FP3, the guide was ignored by almost every driver, with Williams' George Russell posting a time of two minutes and eight seconds for one of his out laps.
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