MiZo Pecs led by as many as 19 points in the first half but had to hold on for dear life at the end as they posted a 66-64 win at USK Praha.
The defeat was a cruel one for the Czech team, who finished the campaign last in Group A with just one victory - not enough to reach the eighth-finals as Dexia Namur climbed above them into fifth place on the night with an upset at home over USO Basket Mondeville, 75-68.
The top five sides from each group go through to the next phase of the competition and the sixth placed team with the best record.
Lotos Gdynia and Famila Schio in Group B finished fifth and sixth respectively, and both advance with 2-8 records.
Hungarian side MiZo, who lay claim to one of the biggest shocks of the season - an 80-68 victory over defending EuroLeague Women champions BC Volgaburmash back on November 3 - went into the game knowing a victory could see them leapfrog Volgaburmash into first place in Group A as the Russians played at Ros Casares on Wedneday evening.
Volgaburmash needed two free throws from Olga Arteshina and then a missed jump shot with four seconds to play from Ros Casares' Janeth to win 59-58.
As a result, even if Pecs had won this game, they would have finished second in Group A as Volgaburmash had a superior points difference from their two meetings, winning the second on 60-43 on December 7.
MiZo Pecs held a huge lead in the first half and went to the changing rooms at the interval with a 35-19 lead.
Praha game themselves a fighting chance by outscoring their visitors 23-13 in the third quarter and made further inroads over the final 10 minutes but came up just short.
Michaela Pavlickova had a game-high 19 points in defeat for Praha, while Albena Branzova poured in 17 in defeat for the winners.