The game in the eastern city of Lublin on Friday marked the first time Cracovia have won the national Cup title in their 114-year history.
Around 3,700 spectators watched the match from the stands at Lublin Arena amid the coronavirus pandemic, Poland's PAP news agency reported.
The Kraków side will next month face off against top-flight league champions Legia Warsaw for the national Super Cup title in a curtain-raiser to the next football season.
Poland on Saturday further eased its coronavirus restrictions, allowing larger crowds at sporting events.
Sports stadiums were given the green light to host fans up to 50 percent of their normal capacity, up from 25 percent under previous rules.
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Source: PAP