The Brazilian driver, who leads the championship, set a 1m27.529s on Thursday morning to top the timesheet at Circuit de Barcelona-Catalunya.
Drugovich, who took victory in the feature race in Jeddah, led from sprint race winner Liam Lawson (Hitech Grand Prix) and rookie Jack Doohan (Virtuosi), who was just three-tenths off the pace.
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All the quickest times of the test came on Thursday morning, with several drivers breaking the 1m28s mark.
Richard Verschoor was fourth quickest overall for Trident, with Ralph Boschung’s time of 1m27.929s from Tuesday afternoon putting him in fifth place.
Reigning F3 champion Dennis Hauger, who stayed with Prema Racing for his debut F2 season, was sixth quickest across the test.
Conditions improved across the three days, as Tuesday’s running saw rain and low track temperatures.
They improved into the afternoon before another wet and windy start on Wednesday, which saw a much-interrupted day of running with seven red flags.
Boschung led the first day of testing for Campos Racing, topping the timesheet ahead of Hitech Grand Prix’s Marcus Armstrong and DAMS’ Ayumu Iwasa.
Running was slow to begin in the opening session, with rain and low temperatures prompting many drivers to reduce their lap numbers.
Drugovich topped the timesheet in the morning, setting a 1m29.755s ahead of ART’s Theo Pourchaire and Iwasa, before the times tumbled for Boschung to go quickest in the afternoon.
DAMS’ Roy Nissany was quickest on Wednesday, battling cold and wet conditions to set a 1m28.812s, more than half a second quicker than second placed Richard Verschoor (Trident).
Armstrong topped the afternoon’s running with a 1m29.752s, finishing 0.208s ahead of Drugovich.
Juri Vips topped Thursday afternoon’s running with a 1m29.288s, over 1.5s quicker than second-placed Jake Hughes (Van Amersfoort Racing).
The Charouz Racing System duo of Enzo Fittipaldi and David Beckmann took third and fourth places respectively.
FIA Formula 3 undergoes two days of testing at the circuit on Friday and Saturday, having undergone another in-season test at Jerez last week.
F2 returns in Imola from 22-24 April.
