The win sees Bologna break into the top ten and snaps Inter's 16 game unbeaten run at home. The forward netted just before the hour to heap more problems on under pressure coach Andrea Stramaccioni, with Inter's fans whistling their own team off at the end. Before this game, Bologna had won just three times away all season.
Protests and jeers whistled around the San Siro as the Nerazzurri struggled to create anything of note in a first half dominated by the visitors.
Fredrik Sorensen headed over moments after the kickoff, then Gilardino hit a half volley just past the post. An Alessandro Diamanti free kick caused problems in the box, but no Bologna player was able to get the final touch to turn the ball into the net.
Antonio Cassano was introduced at the break for the ineffective Marco Benassi to try and give Inter the spark they were missing. It seemed to work initially as Dejan Stankovic just missed getting on the end of a Juan Jesus pull back. The Serbian then found space as he ran towards goal, but his hesitancy to pull the trigger led to his eventual shot being charged down. Stankovic was applauded off the field as he succumbed to an injury.
Bologna hit the front on 57 minutes with a goal that had been coming. Gilardino was played onside by Juan Jesus and Zanetti as he met Diamanti's delivery with a volley which found the corner of the net from eight yards. The forward's evening was cut short just minutes later when he too went off injured.
Manolo Gabbiadini ballooned over a chance to double the lead on 65 minutes. At the other end, Gianluca Curci beat away a Fredy Guarin shot at the near post. Cassano drifted out wide and it took a last ditch block from substitute Naldo to deflect a dangerous shot out of play.
Carrizo was called into action once more eleven minutes from the end. The Argentine palmed over Rene Krhin's header after the substitute's effort bounced off the turf and up towards the roof of the net.
Bologna retreated as Inter threw everything forward. Andrea Ranocchia sent a bicycle kick wide, before the Bologna wall stopped Walter Gargano's 30 yard free kick. Ranocchia and Curci clashed heads as the defender looked to replicate his goal which knocked Bologna out of the Coppa Italia at the start of the year.
Gyorgy Garics cleared off the line after Gargano had bamboozled the rest of the Bologna defence and Curci had the final say, palming clear Esteban Cambiasso's close range header deep into stoppage time.
Inter Milan: Carrizo; Zanetti, Ranocchia, Juan Jesus, Pereira; Stankovic, (Kovacic 55) Gargano; Schelotto, (Cambiasso 65) Guarin, Benassi; (Cassano 46) Palacio
Bologna: Curci; Garics, Sorensen, (Naldo 46) Antonsson, Morleo; Perez, (Guarente 78) Christodoulopoulos; Diamanti, Taider, Gabbiadini; Gilardino (Krhin 61)
Goals: Gilardino 57 (B)