Bianconeri forward Dybala has been the club's top league performer throughout the campaign, though his thunder has been arguably stolen by the arrival of his new team-mate from Fiorentina.
The Argentinian's contract in Turin runs out at the end of June, and attempts to persuade him to sign an extension have so far proven unsuccessful at Juve.
Speaking ahead of his side's vital clash with relegation contender Spezia on Monday (AEDT), Allegri confirmed Dybala would miss the game, and refused to be drawn on the player's future.
"Dybala left training prematurely yesterday," Allegri stated. "He had a problem with his flexor and he did not feel his leg free, so he is still out. If you want I will call him, but he cannot play."
Asked about the forward's injury problems and contract decision, the head coach added: "If we had known, we would have solved it. We are evaluating everything that has been done to understand.
"Then there is the contractual aspect, but it does not depend on me. It will be a negotiation between the club and Paulo. He has been here for eight years and on a technical level, [his contribution] is indisputable."
Vlahovic's arrival in the January transfer window has proven to be one of the more inspired buys of the season across Europe.
But Allegri says the Serbian may take a back seat this weekend, adding: "For Vlahovic I am thinking of the possibility of him starting from the bench. I will see and decide tomorrow."
Elsewhere, the Juve coach weighed in on Paul Pogba, after the Bianconeri were linked with a move for their former player as he appears to wind the clock down on his Manchester United contract.
"Talking about this doesn't make sense," Allegri said. "Pogba is a Manchester United player, I don't know what he'll do next year.
"I had a great relationship with him, he got angry when he lost in basketball and football. Now talking about the transfer market doesn't make sense. Our goal is to reach fourth place."