Both Pogba and Vlahovic are returning from lengthy injury absences and were named on the bench in Serie A on Sunday after they took part in a friendly against a Juventus reserve team earlier last week.
Vlahovic, who had not played for Juve since October, came on for Mattia De Sciglio in the 65th minute of their shock home 2-0 defeat by Monza. Pogba, who has yet to play a game this season, was an unused substitute.
"Apart from (Leonardo) Bonucci who is still out, the only one who won't be available due to a flexor soreness is Pogba," Allegri told a news conference on Wednesday.
"Unfortunately when you're out for a long time and you raise the intensity level, you get pain... Maybe in a few weeks he'll be in top condition.
"He needs his body to readjust and it will take some time, you have to navigate by sight in these situations. From here to the end we have to use him in the best possible way.
"Vlahovic will almost certainly play as a starter, for the others, I have to decide. (The game) can last 120 minutes tomorrow so the substitutions will be even more important."
Juventus, who saw a 15-point deduction for false accounting plunge them from third to 10th place in Serie A in January, need to adjust to their new reality quickly, Allegri added.
"The club will see where we can defend (ourselves), (but) it must not be an alibi or an excuse, we have to go out there and do what needs to be done," Allegri said.
"Maybe it's the first time 15 points have been taken off the table, you were third and you go back down. Now we start again, (and) we have to manage (the situation) as best we can.
"The Italian Cup game has to be done in the best way, we will do our best."
Juve resume their Serie A campaign on Tuesday at 14th-placed Salernitana.
Follow all the action from Thursday's cup quarterfinal on Flashscore.
