Inzaghi's men seemed to be heading for a third straight win that would have seen them go third in Serie A thanks to Nigel de Jong's close-range header midway through the first half on Sunday.
And they were largely comfortable throughout the game but Vincenzo Montella's men grabbed an equaliser out of nowhere courtesy of substitute Josip Ilicic's superb 25-yard drive after 63 minutes.
But despite being disappointed, Inzaghi pointed to pleasing aspects of the performance, and feels that his side is in a better position than many would have expected at the start of the season.
He told Sky Sport Italia: "The result is a little disappointing, but getting this result against a Fiorentina side that has been targeting third place since the start of the season is impressive.
"It was a balanced game and we have some regrets, as we conceded that goal from nowhere by Ilicic. We were coming off two consecutive victories and went close to a third, as aside from the goal we ran very few risks and it was our best defensive performance of the season.
"There are many reasons to be pleased with this performance, but we conceded on our poor clearance in midfield."
The result means that Milan drop to sixth place, but they have gone five without defeat in the league, with the one loss coming in a close contest against Juventus, and Inzaghi believes his team is moving in the right direction.
"I think Milan played on Fiorentina's level, I know we have to improve and build attacking moves better, but we are slowly on the right path," he told Sky Sport Italia.
"I think we did everything we could tonight and you can't build a whole new team in just two months. We are trying to get Milan back to being great, but it takes time.
"If someone had said pre-season we'd be in front of Napoli, Inter and Fiorentina, then nobody would've believed them."