Verstappen was a second up on teammate Alexander Albon, who hit the barriers during the session and braking his front wing - however he was able to return to the pits and continue in the session.
However, Bottas' fastest lap time was set on the soft compound, as was the case with the top three. Charles Leclerc was sixth fastest.
Behind the Ferrari driver was the first of the McLarens, with Carlos Sainz clocking promising pace for the Woking squad. The Spaniard's fastest lap was 1.3 seconds down on the pace laid down by Hamilton.
The stewards noted an incident between Sergio Perez and Kevin Magnussen after the latter was squeezed into the wall as he went to start his hot lap. Perez was also going for a hot lap, as they crawled through the final sector to preserve tyre temperature and wear.
Perez was 13th fastest in the session behind Daniel Ricciardo, but two spots ahead of teammate Lance Stroll, who in turn was behind Antonio Giovinazzi - both Stroll and Giovinazzi set the exact same lap time.
Bahrain International Circuit - Winter testing