Visiting Inter controlled large parts of the first half and it was little surprise when they broke the deadlock.
Diego Forlan and Esteban Cambiasso exchanged passes, before the latter found Giampaolo Pazzini inside the area and the striker made no mistake from close range with six minutes of the first half remaining.
Hosts Bologna came out after the restart with more attacking intent and that was rewarded midway through the second half.
Former West Ham United striker Alessandro Diamanti drew the home side level from the penalty spot after Walter Samuel had fouled Daniele Portanova inside the area with 67 minutes played.
The crucial third goal of the match came with just nine minute left on the clock. Diego Milito, who had been on the pitch for four minutes, was tripped inside the area by Archimede Morleo. The defender was handed a red card for his part and Milito picked himself up to convert the resultant spot-kick.
Lucio confirmed victory for the Blue and Blacks when he turned in Sulley Muntari's free-kick at the near post.