Prior to kickoff both teams observed a minute's silence in honour of late Livorno midfielder Piermario Morosini, who died from a cardiac arrest last week.
The visitors hit Milan on the counter attack and when former West Ham forward Alessandro Diamanti squared the ball for the Brazilian to poke home, Bologna were 1-0 ahead to the disappointment of the home crowd.
Ibrahimovic was at the centre of Milan's attacking threat and felt that he should have had a penalty when he was tugged down in the box.
Nothing was given though and the Swede was frustrated even further when he saw a goal disallowed incorrectly for offside.
However, the Swede was smiling come the final whistle as he snatched the Rossoneri a point in the 90th minute by volleying in Robinho's cross.
With the result, Milan move above Juventus to the top of the table on goal difference but the Turin outfit do have a game in hand.