Frijns, who started Saturday’s race from pole but slipped down to ninth, had led the timesheets after the first runs with a time of 2m04.868s.
He lowered his benchmark in the second half of the session, lapping the Belgian circuit in 2m04.484s to claim provisional pole.
However, Rast denied Frijns pole position with a late 2m01.199s flyer to snatch pole position, as Frijns settled for second place on the grid.
Nico Muller finished another four tenths adrift as Audi locked the top three spots, while Sheldon van der Linde put a BMW on the second row of the grid with a time of 2m04.987s.
Philipp Eng and Timo Glock verified BMW’s improved qualifying showing as they set the fifth and sixth fastest lap time in qualifying, but finished more than a second off the pace of polesitter Rast.
The two BMW drivers demoted Audi’s Jamie Green to seventh, with Marco Wittmann (BMW) finishing just 0.010s behind in eighth.
The top 10 was completed by new BMW recruit Lucas Auer and the Audi of Mike Rockenfeller.
Ex-Formula 1 driver Robert Kubica qualified 12th in an ART-run BMW, behind the factory BMW of Jonathan Aberdein, but ahead of the Audi of Loic Duval, who lost what could have been the seventh fastest time of qualifying due to a track limits violation.
WRT drivers Fabio Scherer and Harrison Newey propped up the field in 14th and 15th places, while their teammate Ferdinand Habsburg failed to set a competitive lap time following his crash in practice on Saturday, which forced him to miss the opening race.
Qualifying 2 results to follow