The Dutchman lasted a little over five months in the job, with Inzaghi, who scored 121 in 294 games for the Rossoneri during his career, replacing his former team-mate on June 9 after the club finished the season in a disappointing eighth place.
Bonera, however, stressed that Milan should be able to look to a brighter future under their new boss, insisting that he is more prepared than Seedorf to handle a role of this magnitude.
"You can see immediately that [compared to Seedorf] there is a significant degree of preparation," the 33-year-old told a press conference at the club's Milanello training centre.
"Clarence had a certain kind of dialogue with players, comparable to [Massimiliano] Allegri, but not great dialogue. Inzaghi places a lot of emphasis on this aspect.
"Inzaghi was an electric player and he has the same characteristic as well as a coach. He seems to be very knowledgeable and has very clear ideas about what should be the way you play on the team. I see he is very taken by this new assignment - I liken him to [Carlo] Ancelotti.
"We are building a new team with a new coach - you could argue that we have the same conditions characterised by Juventus in 2011 when [Antonio] Conte arrived."
Milan endured a torrid season last term, with Allegri sacked in January with the team languishing in 11th, but Bonera hopes that they can turn a corner once the new campaign begins.
"We have great desire to re-emerge," the former Parma centre-back stressed.
"We must recapture the spirit of the old Milan that was scary when it went onto the field against opponents. This year we will have plenty of time to prepare for the big matches - we will not have any kind of excuse.
"We want to create a group of Italians who can develop a sense of belonging to the team, but there were also foreign players in the past that have been able to shape the history of the club."