The French giants improved to 7-3 with the victory.
While Halcon Avenida also finished 7-3 and split their two games with Bourges, the team from France has won the tie-breaker with a superior goal differential.
Bourges opened up a 19-14 lead by the end of the first quarter and extended that to 39-29 by half-time.
They lowered the boom after the restart, outscoring MiZo 19-10 in the third quarter en route to a 27-point triumph.
Endene Miyem led Bourges in scoring with 18 points.
In a solid all-round performance, Bourges guard Celine Dumerc had eight points, seven assists and four rebounds and also came up with three steals.
Anna Vajda had 14 points for MiZo, who came in fourth in Group A with a 5-5 record.
Pierre Vincent, coach Bourges Basket:
"It's always difficult to play against Pecs, but here, at home, it's a different thing. Pecs defended hard but the referees whistled few fouls. We played good defense on Ivanyi to avoid [her shooting for] three points.Players respected all what I asked [them to do]. We played clean with a very tactical defense."
Ákos Füzy, coach MiZo Pécs 2010:
"In the first half, we had a lot of fouls, we lost on that. It was one of the key [stats] of the game. Bourges system tonight was to mainly defend against three player of Pecs and it worked. Bourges defended well and did not let us play our offensive basketball. This year we have a lot of new and young players and it's easier to play at home. They don't have the same feeling in away games. We hope our injured players will come back in time to helps us to reach the quarter-finals."