After completing just six laps and losing over three hours of running on Friday due to his W12 requiring a gearbox change, Bottas took to the Bahrain International Circuit on Saturday afternoon knowing he had ground to make up.
The Finn, however, did not emerge from the garage until after an hour of running, and while he ran wide on his first flying lap on the hard tyre that again appeared to point to the instability of the rear of the car, he made up for it late on.
Bottas, however, had to resort to the softest of the five compounds, the C5, made available by Pirelli to set his leading time of one minute 30.289secs. By comparison, Hamilton's pole lap at the track in November was three seconds quicker.
The 31-year-old, who completed a more respectable 58 laps, edged AlphaTauri's Pierre Gasly by 0.124s, with Aston Martin's Lance Stroll third quickest. Both were also on the C5 rubber.
On another solid day for McLaren, after Daniel Ricciardo had emerged quickest in the morning in the MCL35M - eventually finishing ninth overall on the day - Lando Norris was fourth fastest, albeit on the C4 tyre.
The Monégasque finished 0.597s down on Bottas, but then eight-tenths-of-a-second clear of the next driver on the timesheet in Williams' Nicholas Latifi on the C4,
Red Bull's Sergio Perez enjoyed a solid day albeit bringing out a red flag at one stage in the afternoon session when he bizarrely lost his engine cover while hurtling along the main straight.
Behind ninth-placed Ricciardo was Fernando Alonso on his F1 return, with the Spaniard clocking up 128 laps, just four behind the leading haul from Latifi.
There were also solid outings for rookies Yuki Tsunoda in his Alpha Tauri and Haas driver Mick Schumacher who were 11th and 12th on the timesheet, followed by the Ferrari of Carlos Sainz and Nikita Mazepin in his Haas.
With 11 world titles between them, the timesheet did not make good reading for Lewis Hamilton and Sebastian Vettel, who occupied the bottom two places of the 16-strong timesheet across the day.
Both drivers ran in the morning, with Hamilton completing 58 laps for Mercedes and Vettel just 10 in his Aston Martin due to a change of the Mercedes gearbox that also confined Valtteri Bottas to the works garage for most of Friday morning's session.
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