The victory secured Raków second place in the overall 36-team league table, earning automatic qualification for the knockout stage.
Oskar Repka scored the decisive goal in the 49th minute in Cyprus, Polish state news agency PAP reported.
Raków finished the league phase with 14 points from six matches, recording four wins and two draws and conceding two goals.
However, the club will enter the knockout rounds without coach Marek Papszun, who is set to take over as head coach of Legia Warsaw on Friday.
Two other Polish clubs, Lech Poznań and Jagiellonia Białystok, will compete in the playoff round for a place in the last 16.
Lech secured 11th place with 10 points after a 2-1 win away at Sigma Olomouc in the Czech Republic on Thursday, with Swedish striker Mikael Ishak scoring twice, including one from the penalty spot.
Jagiellonia finished 17th on nine points following a scoreless draw away to AZ Alkmaar.
Legia Warsaw were eliminated despite a 4-1 home win over Lincoln Red Imps of Gibraltar.
Legia ended the league phase in 28th place with six points, having already been assured of elimination before the final match.
The victory was the only win under interim coach Iñaki Astiz, who took charge in late October following the departure of Edward Iordănescu.
Under the Conference League format, the top eight teams in the league table advance directly to the round of 16, while teams finishing ninth through 24th enter a playoff round. Clubs ranked 25th to 36th are eliminated.
Lech will face either Finland's KuPS Kuopio or North Macedonia’s Shkëndija Tetovo in the playoffs, while Jagiellonia will be drawn against Italy's Fiorentina or Croatia's Rijeka.
The draw will take place on January 16 in Nyon, Switzerland, with the playoff matches scheduled for February 19 and 26.
French club RC Strasbourg topped the league phase with 16 points. Also qualifying directly for the round of 16 were AEK Athens, Sparta Prague, Rayo Vallecano, Shakhtar Donetsk and Mainz on 13 points, along with AEK Larnaca on 12.
The knockout rounds will continue in a two-leg format in 2026, with the round of 16 matches set for March 12 and 19.
The Conference League is UEFA’s third-tier club competition but remains important for ranking points and prize money.
Strong recent performances by Polish clubs have earned Poland five places in European competitions for the 2026-2027 season, including two spots in Champions League qualifying.
This season's Conference League final is scheduled for May 27, 2026 in Leipzig, Germany.
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Source: IAR, PAP