The home team was led by the occasional representative of Bosnia and Herzegovina Kenan Kodro with a goal in the third minute of the match.
Zahedi scored once again in the 53rd minute.
Puskas Academy player Baluta received a second yellow card in the injury time and was forced to leave the field.
In the fifth minute of extra time, Stopiro scored the late equalizer for the home side and collected a point for his team.
Puskas Academy sits third in the table, 10 points behind leader Ferencvaros.