The home team took the lead in the 12th minute with a header from Greek defender Pantelis Hatzidiakos, but the visitors responded in the 51st minute when Angolan forward Afimico Pululu scored the equaliser.
Macedonian winger Darko Churlinov netted the decisive goal for Jagiellonia Białystok in the eighth minute of stoppage time on Thursday night.
Meanwhile, Polish top-flight heavyweights Legia Warsaw defeated Spanish side Real Betis 1-0 at home in their Conference League opener on Thursday.
Jagiellonia and Legia will each face six different opponents in the league phase of the 2024/2025 UEFA Conference League until December 19, Polish state news agency PAP reported.
The top eight sides in the league phase of the new-look Conference League will qualify automatically for the knockout stages, while the teams finishing in ninth to 24th place will compete in a two-legged play-off to secure a place in the last 16 of the competition.
Teams ranked 25-36 will be eliminated from the competition, run by European football governing body UEFA.
Source: IAR, PAP, polskieradio24.pl, skysports.com