The Finn led the way on both the medium and soft compounds and finished over two-tenths clear of the field to top the more representative session that took place under the lights at the Losail International Circuit.
Bottas had a faster lap deleted for track limits before he produced his quickest legal effort, a 1m23.148s, during his second soft tyre run.
Just as he was in FP1, AlphaTauri’s Pierre Gasly sat second as he continued his impressive start to the weekend, while championship leader Max Verstappen was 0.350s down in his Red Bull.
Verstappen needed two attempts on softs to outpace title rival Lewis Hamilton, who wound up fourth-quickest and 0.422s adrift of his Mercedes teammate.
As it did during qualifying at Interlagos last weekend, the Red Bull rear wing was seen behaving oddly at the end of the straights. A DRS issue briefly kept Verstappen in the garage before his qualifying simulation run.
McLaren’s Lando Norris got within half a second of Bottas to sit fifth, ahead of the lead Aston Martin of Lance Stroll and Yuki Tsunoda’s AlphaTauri.
Sergio Perez could only set a time good enough for eighth in his Red Bull, with Sebastian Vettel and Carlos Sainz completing the top 10 for Aston Martin and Ferrari respectively.
Traffic once again proved problematic around the tight, fast-flowing Losail track and ruined a number of drivers’ low fuel runs before attention switched to high-fuel race simulations.
Unlike FP1 - which took place during the heat of the Qatar afternoon - FP2 was held at dusk, with lower track temperatures that will be seen again in qualifying and the race.
Haas rookie Nikita Mazepin did not take part in second practice due to a chassis change after he incurred damage to his car over the kerbs in FP1.