The hour-long session had to be red-flagged with 22 minutes remaining following the incident involving the Red Bull and Alpine drivers.
Due to technical issues with the F1 television feed, it proved difficult to determine what unfolded between the duo.
The only replay showed Perez emerging out of Villeneuve with a severely damaged left-rear on the RB16B that forced him into a spin, while following behind and pulling over soon after, Ocon's A521 was showing a broken front right.
Red Bull team principal Christian Horner reported that Ocon was on a slow lap and Perez on a flyer, with contact made between the two, with the stewards to investigate the matter.
Following a 10-minute delay, the 18 remaining cars returned to the circuit for further soft-tyre running, with Bottas edging in front of Hamilton by just 0.041secs with a lap of one minute 16.564s.
Red Bull's Max Verstappen, who had dominated the season-opening weekend in Bahrain before losing out to Hamilton in the race, was forced to settle for the third-quickest time as just 0.058s separated the top three.
On home soil, Ferrari's Charles Leclerc finished almost a quarter of a second down in fourth on the timesheet, followed by AlphaTauri's Pierre Gasly and the second Ferrari of Carlos Sainz, who was less than a tenth of a second behind his team-mate.
Alpine's Fernando Alonso was then half-a-second back in seventh place, with Aston Martin's Lance Stroll, the Williams of Nicholas Latifi and Daniel Ricciardo in his McLaren completing the top 10, with the latter 1.205s down.
From the heat of Bahrain three weeks ago, the teams and drivers were confronted with far cooler climes for the second race of the year, with an air temperature of just 11 degrees centigrade and only 22 on track.
Given the value of getting heat into the tyres, a number of drivers endured spins or offs into the gravel in the opening few minutes, with Perez the first of those, followed by Nikita Mazepin in his Haas and AlphaTauri duo Yuki Tsunoda and Gasly.
The quartet all recovered and made their way back to the pits, although for Mazepin it was the worst possible start to his weekend given the events of his debut in Bahrain when he spun on several occasions in the build-up to a race that lasted just three corners.
Mazepin later brought out a second red flag right at the end of the session when he crashed into a barrier, damaging the VF-21.
Even Hamilton and Verstappen had their off-track moments given the conditions, while Latifi ran off heavily into the gravel at one stage.
Mazepin eventually finished down in 18th, 2.259s adrift, with team-mate Mick Schumacher and Tsunoda bringing up the rear.
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