The Italy international, who scored a hat-trick at the Renato Dall'Ara back in September to give the Rossoneri their first win of the season, put the hosts 1-0 ahead in the 65th minute Sunday, reports Xinhua.
He doubled their lead in the 82nd minute after displaying fantastic individual skill and a predatory instinct in front of goal.
Philippe Mexes gave the hosts cause for concern with a careless own goal in the 84th minute, after which Bologna pushed hard for the equaliser. But Milan managed to hold till the end.
Roma failed in their bid to claim sixth place back from AC Milan as they were held to a frustrating 1-1 draw by Inter Milan at the Stadio Olimpico.
Francesco Totti's penalty put Roma in front in the 22nd minute before Rodrigo Palacio equalised in first-half stoppage time. Roma had the better chances to win but both sides appeared to tire quickly as the game soon fizzled out in the second half.
Roma head coach Zdenek Zeman was still upbeat about his side's chance to qualify for next season's Champions League.
"I continue to say we have to keep playing as there are many games still to go. We do not feel that we are out of the running and hope to prove that on the field," he said.
His Inter counterpart Andrea Stramaccioni was impressed with the draw, saying "It was the right result".
"Roma's potential on home turf is huge both because of coach Zdenek Zeman and the quality of the players," said Stramaccioni.
"They started out very strong and put us under real pressure in the first 20 minutes. After the break I saw a good Inter and I think the draw was the right result. We felt the absence of some of our players in attack," he said.
Napoli failed to make up ground on Serie A leaders Juventus as they had to settle for a 1-1 draw against Fiorentina at the Stadio Artemio Franchi.
Facundo Roncaglia's spectacular goal from within his own half gave the home side the lead in the 33rd minute but Edinson Cavani replied within 10 minutes to join an exclusive club of players with 100 Serie A goals.
Catania's bid to take European football to the Stadio Angelo Massimino next season continued apace thanks to a 2-0 victory at relegation-threatened Genoa.
Chievo restricted Parma to a frustrating 1-1 draw at the Stadio Marc'Antonio Bentegodi that did nothing to boost either side's ambitions for the season.
Cagliari were unable to capitalise on a farcical own goal and Luigi Giorgi's late dismissal as Atalanta got a 1-1 draw at the Stadio Atleti Azzurri d'Italia.
Serie A bottom club Siena recorded a first league win in seven games when they beat Sampdoria 1-0 at Stadio Artemio Franchi.
Pescara remain firmly ensconced in a Serie A relegation battle after losing 0-2 at home to Torino.
