Mauro Icardi twice put the Nerazzurri ahead, with a predatory early goal preceding a magnificent second-half strike, but Michele Pazienza and Panagiotis Kone both dispatched rebounds to earn struggling Bologna a share of the spoils.
The result lifts Davide Ballardini's side two points clear of the Serie A relegation zone ahead of Sunday's matches, while Inter are two points behind fourth-placed Fiorentina and without a win in four games, heaping further pressure on coach Walter Mazzarri.
Milito was given a golden chance to win the game with six minutes remaining after Andrea Mantovani was penalised for tugging down Rodrigo Palacio, but Bologna goalkeeper Gianluca Curci dived to his right to repel the striker's spot-kick.
Yuto Nagatomo was one of three players restored to the Inter team and took just five minutes to justify his inclusion. The Japan full-back delivered a low cross from the left, allowing Icardi to get in front of his marker and stab the ball home. It was the 10th Inter goal Nagatomo has been involved in this season.
Another player recalled to the home line-up, Esteban Cambiasso, then saw an acrobatic, goal-bound volley blocked, before Andrea Rannochia - the other man brought in by Mazzarri - headed just wide.
Bologna gave their hosts a scare on 17 minutes when Mantovani's header went just wide, while Palacio cut inside two defenders midway through the first half and unleashed a drive from the edge of the box, which went narrowly past the post.
Ten minutes before half-time, Bologna equalised against the run of play. Gyorgy Garics produced an exquisite back-heeled nutmeg on the right and cut the ball back for Lazaros Christodoulopoulos.
Inter goalkeeper Samir Handanovic did well to repel the Greece midfielder's shot with his feet, but Pazienza drove the rebound down the middle of the goal and the Slovenian was unable to make a second save.
Shortly after the restart, Danilo D'Ambrosio broke down the right and fired low across Curci's goal and Palacio, sliding in at the back post, was just short of making contact with.
Garics broke away from the Inter defence just after the hour mark, but his shot from the edge of the box failed to trouble Handanovic.
Almost immediately afterwards, Icardi showed him how to score from 20 yards, masterfully curling the ball beyond the despairing dive of Curci and in off the inside of the post.
Inter's lead nevertheless lasted just 10 minutes. Mikael Antonsson swung a high cross into the box from the left, which Cambiasso and Rolando failed to deal with, and when the ball bounced off the latter's chest, Kone fired the loose ball home.
The Albania-born Greece international had scored Bologna's goal in the 1-1 draw with Inter earlier this season.
After 83 minutes, Mantovani brought down Palacio, who had his back to goal, in the area and the hosts had the chance to win it from the spot. However, Curci came to Bologna's rescue.
Substitute Robert Acquafresca could even have snatched a dramatic winner for the visitors, only to be denied by a fine double save from Handanovic right at the end.