The 45-year-old was unable to make a long-term commitment to the Rossoneri as rumours linking him with a move to Roma continue to circulate
The Rossoneri coach faces an uncertain summer despite guiding the club to Serie A's third and final Champions League berth ahead of Fiorentina, as rumours of a possible switch to Roma gather pace.
And speaking after the clash in Tuscany, the former Cagliari boss conceded that Milan are in control of his own destiny as he hailed the team for the progress they have made during his three-year term.
“I have a contract, so when a season ends you talk to the club in order to find out what's next. The club might want to replace me, I don’t know,” he told Sky Sport Italia.
“I certainly can’t walk away, as I have a contract, so it is their decision, but right now talking about the future is too early. The season has just ended so let me enjoy this victory!
“Right now I want to talk about the game, what happened this evening and what the team achieved with 42 points in the second half of the season.
“In three years the president has put his faith in me and could so easily have fired me this season after the first eight games. We have introduced many new young faces to the mix and helped the older guard too, so Milan have solid foundations.
“In my three years at Milan we have picked up many points, so at the end of the day what counts are results. I think we have achieved our objectives in the circumstances.”
Milan were trailing Siena and seemed to be heading for the Europa League until the latter stages of the second half when they were awarded a controversial penalty, but Allegri claimed that the decision balanced out previous calls against his side.
“During a season, you get some penalties that are dubious and others that are stonewall but not given. We were two points ahead going into the weekend, our destiny was in our hands, so we got the victory,” he added.
“It was normal to be a little tired, especially psychologically, after this incredible fightback from a poor start to the campaign.
“We were faced with a great goalkeeper and hit the woodwork, while we were a little too hasty and felt the tension of the occasion.
“I want to thank the players and the fans, who deserved a night like this. Stephan El Shaarawy was on the bench because he did not seem to be in good shape, while we needed someone with Robinho’s characteristics."