The Indian driver set the session's early pace with a 1:50.724 lap to hold the early advantage; before stretching the pace to 1:50.576 at the sessions halfway point.
However, just as the session reached its climax Daruvala was bettered by Hughes, with the Brit setting a time of 1:49.519, to edge the Prema driver by 0.087s.
Championship leader Robert Schwartzman completed the top three; albeit over a quarter of a second away from adding to his Pole from Barcelona.
Marcus Armstrong and Leo Pulcini made up row three, with the Italian making up for his Barcelona tribulations.
However, it was a poor day for ART, with all three of their drivers missing out on a top ten start. Christian Lundgaard led the French squad's challenge in a reserved 12th, with fellow Renault-academy prospect down in 14th.
Bahrain International Circuit - Winter testing
Would you like to stay up to date with the latest Lewis Hamilton and Formula 1 news from GPtoday? Activate free push notifications and be the first to know!