Chief executive Giorgio Furlani, sporting director Igli Tare and technical director Geoffrey Moncada have all been relieved of their duties alongside Allegri, with American investment group RedBird Capital confirming the departures in a blunt public statement issued on Monday.
"The final stretch was completely inconsistent with the performance up to that point, with last night's disappointing loss in the final game turning the season into an unequivocal failure," RedBird said.
"It is now time for change and a comprehensive reorganisation of football operations."
Milan had needed just a point from their home match against Cagliari on Sunday to secure a top-four finish. Instead they conceded twice after taking the lead and lost 2-1, dropping to fifth in the final Serie A standings.
The result allowed Como — a club competing in European football for the first time in their history — to leapfrog Milan and claim the fourth Champions League place. Inter Milan, Napoli and Roma took the top three spots.
For the second year running, Milan will play Europa League football.
Allegri, 58, had returned to the club last May tasked with reversing a season in which Milan finished eighth under Sergio Conceicao. For much of this campaign he appeared to be succeeding — Milan spent the majority of the season inside the top two and were considered genuine Scudetto contenders before losing seven of their final 13 matches as Inter claimed the title for the second time in three seasons.
It was his second spell at the club. Allegri managed Milan between 2010 and 2014, winning Serie A in 2010-11 and the Italian Super Cup the following year.
Tare joined Milan only last summer alongside Allegri, meaning both men depart inside 12 months. Moncada had been part of the club's scouting and technical structure since 2018, rising to technical director in 2023. Furlani had served as chief executive since 2022, effectively representing former owners Elliott Management before RedBird's takeover.
Special adviser Zlatan Ibrahimovic was the only senior figure spared in the overhaul.
RedBird managing partner Gerry Cardinale is now expected to work with Ibrahimovic to identify a new head coach, chief executive and sporting director ahead of next season.
"Further announcements regarding the next appointments will be made in due course — with the goal to be ready and well-prepared for the next season," the statement concluded.