The game at the National Stadium in Warsaw on Wednesday marked the second time Jagiellonia have won the national Super Cup title.
The club's Spanish right-winger Miki Alonso scored the only goal of the match in the 14th minute, Polish state news agency PAP reported.
The one-off Super Cup match is traditionally held between the winners of the Polish Cup and the Ekstraklasa premier league champions from the previous season.
Jagiellonia in May last year won Poland’s top-flight Ekstraklasa football league for the first time, while Wisła beat Pogoń Szczecin 2-1 in the Polish Cup final.
The Super Cup clash is traditionally held as a curtain-raiser to the new football season, but Wednesday's game—originally scheduled for July last year—was postponed multiple times due to both teams' commitments in European competition.
The national football association ultimately rescheduled the match for April 2.
Jagiellonia will next Thursday face Spain's Real Betis away in the UEFA Conference League quarterfinals.
(gs)
Source: PAP