The MP Motorsport driver took provisional pole early on in the session, setting a 1m32.838s to take the top spot.
Several other drivers, including Arthur Leclerc, were set to improve on their times when the red flag was waved after Carlin’s Zak O’Sullivan came to a halt on the start-finish straight.
With just two minutes left on the clock, the field emerged for a dash to the line to make their last attempts, but traffic caused many to miss out, including championship leader Victor Martins, all three Prema cars and Isack Hadjar.
Smolyar did make it around in time for a final lap, improving to 1m32.740s to secure pole.
Van Amersfoort Racing’s Reece Ushijima shot up to second before having his final lap deleted, leaving him in 19th place, and promoting Zane Maloney (Trident) to second.
Despite traffic problems, Ollie Bearman and Leclerc will line up on the second row.
Franco Colapinto was first out on track for Van Amersfoort Racing to lead the 30-minute qualifying session, with Carlin’s Jonny Edgar first to set a flying lap of 1m34.457s.
He was quickly toppled by Caio Collet, 0.9s quicker, with Hadjar slotting into second as the Prema cars pitted without setting a flying lap.
Edgar briefly reclaimed the top spot with a 1m33.319s, before Smolyar went top again, leading from Bearman, Leclerc and Kush Maini (MP Motorsport).
The field pitted again with 10 minutes remaining, with Leclerc and Bearman first out for Prema in clear air.
But the red flag ruined any chances of improving, with Leclerc having been setting a purple middle sector while Ushijima was flying in the first.
With two minutes left on the clock, the field raced out the pits in a bid to cross the line before the chequered flag, with Martins last out the pits.
A slow running Jak Crawford hindered both his team-mates, leaving all three Premas unable to set a last lap, the Red Bull junior lining up seventh for Sunday’s feature race.
ART’s Gregoire Saucy will line up fifth, with Maini in sixth and Martins in eighth.
Euroformula Open championship leader, Oliver Goethe, taking part in his first F3 weekend in place of an injured Hunter Yeany, will start on pole for Saturday’s reverse-grid sprint race, with Franco Colapinto in second and Hadjar in third.
F3 Hungary: Full qualifying results
