The Czechs went on an all-assault attack since that paid off. Daniel Kolar equalized in the 76th with a header off a Pavel Horvath precise cross.
Alan Dzagoev was sent off in the 67th for a foul from behind on Vaclav Prochazka and Pontus Wernbloom followed him in injury time after pushing a player to the ground to set up a CSKA free kick in an emotional finish.
"It was all about emotions," Plzen coach Pavel Vrba said.
The match was a farewell for Vrba who takes over the Czech national team in January. The 50-year-old led Plzen to the lucrative Champions League twice in the last three years. Plzen also became the first Czech club to extend their European campaign into spring for the third straight year.
"It's a great success for us, we're changing the history of Czech football," Vrba said.