The game was initially suspended while Juankar received medical treatment before he was taken away on a medical cart.
The match between two of the biggest teams in Greece has a reputation for violence on and off the pitch.
The fixture was abandoned in 2019 after Panathinaikos fans attacked players on Olympiacos' team bench and clashed with police outside the OAKA Stadium. Olympiacos were subsequently awarded the victory.
In Sunday's match, both teams returned to their respective changing rooms after Juankar was struck by the firework and play was suspended for around an hour.
The decision to abandon the game was relayed to the crowd inside Olympiacos' Georgios Karaiskakis Stadium at around 21.30 PM local time, more than three hours after play was suspended.
After the announcement to abandon the match was announced, Panathinaikos' official X (formerly Twitter) account posted: "The referee closed the match sheet and the fate of the match will be decided in the courts..."
No decision on the outcome of the fixture has yet been communicated by the Greek Football Federation.