Dybala made his return from an absence of six weeks due to a hamstring injury in Juve's 1-0 derby win at Torino last time out, with Higuain substituted early in that game after picking up a fitness problem of his own.
Higuain is expected to miss the home match against Atalanta and, although his ankle injury is not serious, Dybala will not necessarily replace him.
Allegri's men face Atalanta again in the second leg of their Coppa Italia semi-final on Wednesday and then take on Tottenham in the return fixture of a Champions League round-of-16 tie early next month, with the Juventus coach planning to reintroduce Dybala to action gradually.
Juan Cuadrado and Mattia De Sciglio are ruled out of the Atalanta match and Allegri confirmed Federico Bernardeschi may need surgery on a knee injury, although Blaise Matuidi is back from a thigh issue.
"It will be difficult for Higuain to play tomorrow," Allegri told reporters on Saturday.
"Bernardeschi will be re-evaluated in the coming 20 days. If by that time the conservative treatment has not had the desired effect, we'll see if he needs an operation. Unfortunately, that is the situation with Federico. Apart from De Sciglio and Cuadrado, everyone else is at my disposal.
"Yesterday [in training] I tried Dybala in the striker role, but it's unthinkable that after 40-45 days of not playing that he can play the full 90 minutes for the next three games, so we'll have to manage him carefully.
"He played around half an hour against Torino, so it's about finding the right fitness levels in a decisive moment of the season.
"Matuidi and [Miralem] Pjanic will play tomorrow, and then I'll choose one of [Rodrigo] Bentancur, [Claudio] Marchisio or [Stefano] Sturaro to play with them. Bentancur has a great future ahead of him, he's 20 years old and has a lot of great quality, he will be a major player for Juventus.
"[Gianluigi] Buffon will play tomorrow, as will [Stephan] Lichtsteiner and I'll choose one of [Mehdi] Benatia or [Daniele] Rugani."
Atalanta are winless in four games in all competitions ahead of Sunday's trip to Turin, with Gian Piero Gasperini's men exiting the Europa League on Thursday despite a 1-1 home draw with Borussia Dortmund.
"Compliments to Atalanta with how they handled the Europa League," Allegri added. "I'm sorry that they were eliminated. Italian teams need to move forward in Europe even if it is very difficult.
"Atalanta will want to get right back at it - and Wednesday like us they will be fighting to reach the final of the Coppa Italia. They are a very physical team that plays well and we will have to handle them in the right way.
"Tomorrow is the first game of an important cycle of matches before the international break from here until our game with SPAL [on March 17]."