Beganovic made an impressive start to the F3 season, backing up his strong performance in free practice by setting the fastest time in the first qualifying session of the year.
Williams Academy driver Luke Browning was second in his Hitech entry, falling 0.167s short of the 1m46.431s pole time of his Prema-entered rival.
ART driver Laurens van Hoepen will start the first race of the year, Friday's partial reverse-grid sprint offering, from pole position after qualifying in 12th.
The session began poorly for Joshua Dufek, who was forced to return to the pits following the first of his two warm-up laps with a transponder issue on his PHM AIX Racing entry.
It briefly appeared that he could have been granted a reprieve as Campos Racing driver Oliver Goethe took too much kerb at Turn 3 on his opening flying lap and caused his car to shut off.
Despite coasting up the straight to Turn 4, Goethe was able to get his engine started again without causing a red flag that could have benefited Dufek.
Dufek later found himself under investigation for touring the support race pitlane during the moment of strife.
Source: Autosport