Charles Leclerc suffered early in Q1 after his first time was deleted for exceeding track limits, while Mercedes led out front on the medium compound tyres.
As a result, Vettel did not make it into Q1, starting tomorrow's race in seventeenth position.
Only two-tenths separated sixth to twelfth after everybody had done their first runs, with McLaren's Lando Norris fearing the second run would get 'messy'.
At the beginning of Q3, Hamilton led teammate Bottas by just over a second, while Red Bull's Albon once again had his time deleted once again for running wide at Parabolica.
On their second run, Hamilton once again got ahead of Bottas by 0.7 of a second for pole position, with a time of 1:18.887,
.McLaren's Sainz was best of the rest, pulling off a very quick lap to take third for the team ahead of Racing Point's Perez.
Bahrain International Circuit - Winter testing