Bayern Munich and Manchester City had already earned progression to the knockout stages of Europe's premier club competition, with the Europa League spot the only issue to be decided in the final round of Group D matches.
Pavel Vrba, who was taking charge of his final Plzen match before assuming control of Czech Republic's national team, saw his side come from behind in dramatic fashion after Ahmed Musa's 65th-minute header put CSKA in front.
CSKA's Alan Dzagoev was dismissed for a clash with Vaclav Prochazka, and Plzen soon levelled through Daniel Kolar before Tomas Wagner scored a winner in the final minute of normal time.
There was also time for Pontus Wernbloom to be shown a red card as Plzen extended their European campaign into the new year for a third consecutive season.
Zoran Tosic of CSKA and Plzen’s Pavel Horvath had early opportunities, but each fired over the crossbar.
CSKA brought Milan-bound Honda into the action seven minutes into the second half and, a minute before the hour mark, Dzagoev's long-range strike was too hot for Kozacik to handle, forcing a clearance from Prochazka.
The lively striker peeled away at the far post before heading Honda's cross into the ground, but Dzagoev's dismissal for an off-the-ball incident with Prochazka made life uncomfortable for the visitors as Plzen pressed forward.
They were eventually rewarded when Kolar headed home unmarked from Horvath's cross with 14 minutes remaining.
Wagner then converted Frantisek Rajtoral's delivery in the dying stages of the game to ensure Vrba's reign ended on a notable high.
