Neither driver managed to set a time in qualifying set-up on the soft tyres, with Bottas running wide on the exit of turn one on his run, while Hamilton exceeded track limits on his flying lap.
The Finn still finished top of the timesheet with a lap of one minute 36.276s, two-tenths of a second clear of Hamilton, both on the medium compound, as was Max Verstappen in his Red Bull who was third quickest, 0.770s down.
The session ended bizarrely for Hamilton as he stopped in the pitlane in front of the Haas pitbox, complaining he was unable to find any gear.
As his crew raced to help him, Hamilton removed his steering wheel, placed it back on and was able to resume. Earlier in the session, the seven-time champion had swapped his steering wheel completely before continuing.
In conditions more representative of those that will be encountered for qualifying and the race as dusk settled over the track, compared to the afternoon sunshine for FP1, the session was not plain sailing for all the teams.
Just before Raikkonen's engine caught fire, George Russell also encountered his own PU issue, resulting in his crew changing the battery.
Behind the leading trio, Red Bull's Alex Albon was fourth quickest, finishing a quarter of a second behind team-mate Verstappen, with McLaren's Lando Norris then at the front of a queue of eight drivers who were covered by under two-tenths of a second, down to team-mate Carlos Sainz in 12th.
Raikkonen ended up 13th in the standings, 1.792s behind Bottas, while Russell was 18th on his return to Williams after his substitute role for Hamilton in the Sakhir GP, with the Briton 2.541s down. Team-mate Nicholas Latifi brought up the rear.
The session started with all drivers running the rule over one of Pirelli's compounds for 2021, with each required to complete at least eight timed laps.
It resulted in an impromptu tyre test for the 20 minutes, which culminated in Bottas and Hamilton finishing a second clear of the field.
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