Dybala was an unused substitute at the Allianz Stadium as a late brace from Gervinho saw Juve make a rare slip up in their Scudetto defence and the Argentina forward left the bench before the end of the game.
Afterwards, Allegri joked Dybala was cold but was privately reported to be furious with the player's actions, with the matter coming to a head at training on Thursday.
"He apologised, as it was right to do from a clever boy like him, to whom the club has given important responsibility – the number 10 jersey and the captain's armband when [Giorgio] Chiellini is not available," Allegri said at a news conference to preview Juve's trip to Sassuolo.
"He had an attitude that is not appropriate, he understood that. Case closed."
Allegri went on to discuss the challenge posed to Dybala by Cristiano Ronaldo's arrival and how it has altered the make-up of the Juventus attack.
"His position on the field has not changed, only the characteristics of those who play alongside him have," he said.
"The difference is that last year there was [Gonzalo] Higuain and [Mario] Mandzukic; this year there is Ronaldo and Mandzukic.
"He touches the same amount of balls, has the same opportunities. I do not tell him to be a full-back.
"Sometimes you try to find things that do not exist. I laugh when I read certain things but people like to fill their mouths. I listen and enjoy it.
"Tomorrow Dybala or [Federico] Bernardeschi will play. If Dybala plays, he could be the captain but I have to decide."
It has been an eventful weekend off the field for the Serie A champions, with winger Douglas Costa emerging unhurt after crashing his car on Monday.
The former Bayern Munich and Shakhtar Donetsk star has struggled for his best form this season since serving a four-match ban handed out for spitting at Sassuolo's Federico Di Francesco in this weekend's reverse fixture.
"It's a strange situation with Douglas Costa. He started the season very well, then did that stupid thing against Sassuolo and was suspended," Allegri explained, having withdrawn the Brazilian through injury at half-time against Parma.
"Then he got injured against Valencia. He needs time to get into the condition and on Saturday he got injured again.
"The rest is private life. The players have time to do everything, they're boys but they have to be good at managing those moments, claiming a higher level of attention.
"Private life management matters, these are things that happen. Fortunately, nothing happened to anyone [in the car accident]. Now we have to be at the top of our physical and mental condition."
Allegri teased the return of Juve's fabled "BBC" defensive line-up of Andrea Barzagli, Leonardo Bonucci and Chiellini being close after Barzagli returned to training. However the 37-year-old's target at this stage is next weekend's game against Frosinone.