Dybala was left upset after their 3-3 draw with Parma last week, refusing to see the final minutes of the game from the bench.
“Dybala has apologised, as was only to be expected from an intelligent lad like him," said Allegri.
“The club gave him a lot of responsibility with the Number 10 jersey. Paulo has understood the situation, so the case is closed."
Allegri also disputed suggestions Dybala was being played out of position to accommodate Cristiano Ronaldo.
“He has always started and finished moves, it's just this season he missed or forced a save where last term the ball went into the net. I listen to all this chatter about tactics and it amuses me.