The home team's Angolan forward Afimico Pululu scored both goals of the match in the 69th and 72nd minutes at the Municipal Stadium in the northeastern Polish city of Białystok, public broadcaster Polish Radio’s IAR news agency reported.
Jagiellonia beat Danish top-flight side FC Copenhagen 2-1 away from home in their opening game of this season’s Conference League in early October.
The Polish champions, coached by Adrian Siemieniec, will face Norwegian side Molde in their next Conference League fixture in Białystok on November 7.
Meanwhile, Polish top-flight heavyweights Legia Warsaw defeated Serbian outfit TSC Bačka Topola 3-0 away in their second Conference League league phase fixture on Thursday night.
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