At the beginning of the session the track was perilously wet in places yet relatively dry in others.
With conditions constantly improving it seemed as though whoever crossed the line last would take pole.
McLaren protege and ART Grand Prix driver Vandoorne took this too literally.
Vandoorne: I had to dominate GP2
The Belgian, who was blocked by Status Grand Prix's Marlon Stockinger on what was going to be his penultimate lap, slowed down to gear up for one final run.
But he left it marginally too late and crossed the line less than a second after the chequered flag fell, meaning he would have to settle for second.
DAMS driver Lynn, who watched on from the pitlane, grabbed pole on his last run to edge out Vandoorne by just 0.038 seconds.
Alexander Rossi qualified in third but was 0.301s off the pace. The American, fresh off the back of two F1 races with Manor, struggled throughout the session but ran consistently in the lead group.
Red Bull junior Pierre Gasly ended the session fourth, despite leading the field on several occasions, ahead of fellow countryman Arthur Pic who also headed the order for a spell.
Johnny Cecotto, who had previously announced his retirement, was sixth ahead of Trident team-mate and Ferrari protege Raffaele Marciello. The Italian lost out on one quick lap when he was stuck behind GP2 debutant Dean Stoneman.
Richie Stanaway was briefly fastest as others came in for a mid-session pitstop.
The Kiwi couldn't maintain his place though and had to settle for eighth, edging out Norman Nato and Sergey Sirotkin, who once again struggled to keep his Rapax car on track at his home event.
Stanaway's fellow New Zealander Mitch Evans struggled in the session and will start 18th, behind his Russian Time team-mate Artem Markelov.
Vandoorne seals GP2 title in Russia
Rossi wins after Lynn crashes out