Petrov, who made 228 league appearances for Celtic, believes that Boyata's Celtic career is over after he claimed that he was unable to travel for their Champions League Qualifier.
A 2-1 defeat crushed any Celtic hope of qualifying for the Champions League group stages for the third successive year, boss Brendan Rodgers said after the game that Boyata was in fact fit to play.
It is believed that Boyata's agent is trying to engineer a move out of Celtic Park, with Seville interested.
"The Boyata situation has cost Celtic because he was a big part of their defence," said former midfielder Petrov.
"If you had him at AEK, it could have been a different score," Petrov told 'Sky Sports News'.
Asked if there was any way back for Boyata at Celtic, Petrov said: "They've definitely missed him. If he had been in the team there would have been a completely different outcome.
"Also missing (Moussa) Dembele and (Odsonne) Edouard cost them, they're big players for the club.
"But if he refused to travel it would be very difficult for Dedryck to go back in that team. You let your team-mates [down], the players you actually spend every single day with. It will be difficult.