The veteran goalkeeper has a calf complaint, while midfielder Pjanic is struggling with a muscle strain, and both are doubts for the meeting with the Greek champions.
Mario Mandzukic is fit again after missing the win over Napoli, while Gonzalo Higuain will also play, but defender Giorgio Chiellini is not in the squad for the match in Athens, leaving Allegri with some concern about his options.
"Higuain will play, he's fine physically and mentally. Mandzukic is back," Allegri told a news conference.
"There are two problems: Buffon and Pjanic. Miralem has a muscle strain; Gigi has a calf problem but, if he can't play then [Wojciech] Szczesny will play.
"With Chiellini out, one of Mattia De Sciglio or [Daniele] Rugani will play. If Pjanic doesn't play, we have [Claudio] Marchisio, [Rodrigo] Bentancur and [Sami] Khedira."
A win will guarantee Juve progress to the last 16 along with group winners Barcelona, but a defeat would allow Sporting CP the chance to climb above them into second place if they beat the Catalans at Camp Nou.
But Allegri, whose side ended Napoli's unbeaten run in Serie A on Friday, has urged his players to ignore the Barca result and focus simply on beating Olympiacos.
"It's more important than Napoli because we have to win," he said. "We need to show respect and we don't need to think about what will happen in Barcelona."
Olympiacos are guaranteed to finish bottom of Group D, having lost four and drawn one of their first five games, but head coach Takis Lemonis wants them to put on a special display for their fans.
"Certainly, we are in a bit of a special situation, but first of all there is the prestige of the game; secondly the points are important for our UEFA nation ranking," he said,
"Another point is we must always have the incentive to play well. Of course, I'm not troubled about incentives. In any case, it is important to be completely focused and play our best game."