Wednesday night's 69-64 win improved Prague's record to 4-6, but they have an inferior goal differential against Lotos PKO BP who are also 4-6 and that means a fourth-place finish and Eighth-Finals clash for the Czechs against Spartak Moscow Region.
Because of Lotos PKO BP's 14-point triumph in the first leg, Prague needed to win big to avoid Spartak, and in the third quarter that looked possible.
The game was knotted at 33-33 at half-time, but Lubor Blazek's Czechs held Lotos to just six points in the first seven minutes of the third quarter and opened up a 56-39 advantage.
Lotos PKO BP finished the quarter on an 8-1 run to trail 57-47 and nearly came all the way back in the fourth.
Emilija Podrug's two free throws cut the Polish team's deficit to 63-62 with 3:14 remaining.
Sonja Kireta, who had 18 points and seven rebounds for Prague, replied with a jumper and Lotos PKO BP got no closer than three points the rest of the way.
Alana Beard poured in 20 points for Lotos PKO BP.