A late lap from the Australian in fading light saw the Virtuosi pilot climb the order in difficult mixed conditions.
Juri Vips claimed a maiden F2 pole position and will be joined on the front row by fellow Red Bull-backed youngster Ayumu Iwasa.
Vips claimed pole by little more than a tenth of a second from Iwasa, his time coming with six minutes remaining in the session and following a red flag when Olli Caldwell spun.
Formula 2 qualifying following the delayed F1 session, with rain again falling as cars headed out, forcing drivers onto wets.
Ralph Boschung, who set the pace in the afternoon practice session, was the first driver to lay down a marker but after the opening round of laps, it was Clément Novalak who was fastest.
Van Amersfoort Racing's Jake Hughes then moved to the top of the timesheet, before being displaced by Vips.
Then came the interruption for Caldwell, following which Boschung improved on his earlier time only for Vips to finally stamp his authority on proceedings with a time that would not be beaten.
Boschung ultimately fell to fourth as Iwasa and Doohan also improved late in the session.
But while Vips will start Sunday's race from pole position, it will be Armstrong who lines up first for Saturday's Sprint Race.
Featuring a reversed top eight, that will see Logan Sargeant alongside him on the front row, with Doohan starting out of eighth.