Sebastian Vettel failed to set a lap time in Q1 as he had issues relating to his turbo, which hit as he took to the circuit for the first time.
The German is set to start his home Grand Prix from the back of the grid, following on from a strong weekend for the Scuderia outfit up to this point.
Charles Leclerc stormed his way into Q3 and was in the running for pole before he too was hit with problems that saw him clamber out of his car before he took to the circuit in the final stage.
Bottas secured third place, ahead of Pierre Gasly, who had his fastest time in Q3 deleted, which would have put him one-tenth away from the front-row. However, he didn't lose any positions from having his time deleted, and will line-up on tomorrow's grid in fourth place.
Kimi Raikkonen was close to getting onto the second row as his time was narrowly slower than Gasly's for fifth place.
Sunday's race gets underway at 15:10 local time, as Mercedes goes in search of its 10th win of the season.
Bahrain International Circuit - Winter testing