The Viola stunned Milan 2-1 at the San Siro.
"It was an unexpected defeat and a complicated game thanks to Fiorentina. We felt tired, but once we had taken the lead the equaliser came far too quickly," said Allegri.
"It was a generous penalty, but then the referee gave back that generosity with his decision on Cassano. There has been too much talk about referees lately and I think everyone should accept decisions in a calm manner.
"There was too much haste in trying to win the game, so we went for long balls when I was asking for short passes. It's a shame that we lost, because now Juve have the chance to go in front, although there are still seven games to go.
"It is not true that the Champions League elimination to Barcelona affected us, as we have immediately put it behind us. More than anything else, it was a waste of energy.
"The only thing we could've done here was come out better for the second half. We must accept the defeat and resume with more determination.