As qualifying action resumed in earnest over the final minutes, Andlauer hit the front with a 1min 47.847sec run and Al Faisal climbed to fourth with a 1min 48.241sec, as Ellinas snatched third behind Ammermüller.
With two minutes left on the clock, Pereira displaced Al Faisal with a 1min 48.234sec run and Ellinas claimed provisional pole with a 1min 47.780sec tour. Mawson also moved in front of Al Faisal who slipped back to seventh after Ten Voorde carded a potent lap.
Ellinas had done enough to claim pole from Andlauer and Ammermüller, with Al Faisal qualifying behind Ten Voorde, Mawson and Pereira in seventh place.
But the results were changed after the session finished and Andlauer was awarded pole with Ammermüller, Ten Voorde, Ellinas, Pereira and Al Faisal as the next best five.
Earlier, drivers had to cope with heavy rain during the practice session on Friday. Andlauer mastered the conditions to card a best lap of 2min 03.134sec during his 18 laps on the slippery circuit.
Al Faisal ran for 17 tours of the circuit and a best run of 2min 04.743sec put the Omani into 12th among the 31 starters.