CSKA midfielder Alan Dzagoyev opened the scoring in the 31st minute, and Yury Zhirkov added a second for the Russian side in first half injury time.
Bosnian midfielder Semir Stilic scored for the Polish side in the 66th minute, bringing the scoreline to 2-1.
The victory followed convincing wins for CSKA against Spain's Deportivo and the Dutch side Feyenoord in the UEFA Cup group stage. The match was the former Red Army side's last home game of the season.
CSKA's cross-town rivals Spartak face Croatia's Dynamo Zagreb later this evening.
Spartak lost their first UEFA Cup match 2-1 at home to Italian club Udinese, while Zagreb have had mixed results, beating NEC 3-2 at home before going down 4-0 to Tottenham in London. The game kicks off at 8:45 local time (10:45 p.m. in Moscow).
Having finished in eighth place in this season's Premier League, Spartak are bottom of their UEFA Cup group, and desperately need a good performance away to Dynamo Zagreb to kickstart their campaign, with games against Tottenham Hotspur and Holland's NEC still to come.
Russian clubs have established a good record in the UEFA Cup, which will be revamped as the Europa League next season, with CSKA's 2005 triumph followed by Zenit St. Petersburg's lifting of the trophy this May.
Zenit will enter the UEFA Cup from the knockout stages after failing to get out of their Champions League group, finishing behind Juventus and Real Madrid.