It had been a weekend of dominance for Dunne in Belgium, who topped the practice session and qualified on pole in dry conditions by 0.421 seconds.
He gained two points on Verschoor for pole position and chipped another two points out of the Dutch driver's lead by finishing seventh in the reverse grid sprint race.
Rain hit the Belgian circuit on Sunday morning, to the extent the Formula 3 race had to be cancelled, but conditions cleared up to allow the F2 race to get under way behind the safety car - a different start procedure that ultimately led to his penalty.
Dunne pulled out a four-second lead once racing started and, despite a brief challenge from Japan's Ritomo Miyata, he maintained his lead for the mid-race pit stops.
His Rodin Motorsport team produced a fast pit stop to get him back into the race in fourth place, behind drivers who had yet to stop.
Dunne then produced a stunning overtake around the outside of Pouhon bend past Ollie Goethe to re-take the lead and pulled away from Stanek and Lindblad.
There was a late safety car for Sebastian Montoya, who spun at Eau Rouge with five laps remaining.
The Colombian's car was still being recovered when Goethe's engine expired with two laps to go, which meant race control red flagged the race and Dunne was able to take the chequered flag unchallenged.
However, Dunne was handed the penalty for the infringement at the start of the race behind the safety car.
FIA documents say that his Rodin team "decided not to activate the set-up procedure" and that Dunne checked with his engineers before setting off from the grid.
The error was costly in what had been the most complete performance of Dunne's rookie Formula 2 season to date, but the penalty now leaves him 11 points off Fornaroli.
It is the second time Dunne has lost a podium finish in three rounds after he was disqualified from the feature race in Austria after excessive plank wear on the skid block of his car.
The 11th round of 14 takes place in Hungary next weekend.