The leading pair finished more than 16 seconds ahead of Danilo Petrucci, who rounded out the podium for the third time in the round.
Britain’s Sam Lowes was fourth and remains sixth in the championship standings.
Rea was involved in an incident at the first corner which brought about a yellow flag.
The six-time champion, who made his return from injury at the Italian round two weeks ago, was ultimately penalised for the collision which left Alvaro Bautista and Xavi Vierge unable to finish the race.
After finishing 10th in the round’s previous two races, Rea earned three points to take both his weekend and season’s total to nine.
Bulega leads the standings on 252 points with two-time champion Razgatlioglu 31 behind.
The sixth round of the championship will take place at Misano between 13 and 15 June.
