Bottas finished with a leading lap of one minute 23.148s at the Losail International Circuit, finishing 0.209s ahead of AlphaTauri's Pierre Gasly, with F1 title contenders Max Verstappen and Lewis Hamilton off the pace in third and fourth.
Mercedes driver Bottas has shown a new lease of life since the announcement was made in August he would be leaving Mercedes at the end of the season to join Alfa Romeo, taking three of the last four poles in particular.
On a smooth circuit, the type of which enjoyed by Bottas, he was the leading runner on both the medium and soft compound tyres.
Unsurprisingly, the conditions in FP2 were markedly different and representative of what the drivers and teams will encounter during qualifying and the race.
Under the evening lights, compared to the warm afternoon sunshine for FP1, the track temperature was the most significant change with a drop of 10 degrees.
That arguably played more to Mercedes' strengths, in tandem with a fast, flowing circuit dominated by medium-to-high-speed corners.
After leading the way by almost three-tenths-of-a-second over Hamilton on medium tyres with a lap of 1:23.324s, Bottas was the first of the frontrunners to switch to the softs.
He initially shaved over two-tenths off his time with a 1:23.154s, only for it to be deleted for exceeding track limits at turn seven.
When Hamilton followed on his first set of softs for the session, surprisingly there was only marginal improvement before Gasly slotted in to split the pair, 0.033s down.
Bottas' second attempt, though, was legal as he stretched his advantage to 0.209s, carrying a more incisive line through the turn eight-nine chicane, and in turn exiting with more speed.
Verstappen and Hamilton, arguably holding something in reserve ahead of qualifying, finished 0.350s and 0.422s adrift of Bottas respectively.
McLaren's Lando Norris and Aston Martin's Lance Stroll, who both missed out on time in FP1 due to sensor and hydraulic issues in their cars respectively, finished fifth and sixth quickest, around half-a-second back.
AlphaTauri's Yuki Tsunoda has fared well so far, and was 0.537s down in seventh, followed by Sergio Perez in his Red Bull. The Mexican has appeared off the pace to date.
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