Beaten in the first encounter on December 1 at FMP, 82-74, Tuesday's result has left both sides with 4-1 records.
The 11-point win is good enough to give Banvit a higher placing should the two sides win their remaining games.
Trailing 58-57, Banvit reeled off the last nine points over the final 1:18 of the third quarter for a 66-58 advantage.
They stayed comfortably ahead the rest of the way.
Lance Williams had 19 points for Banvit, who also got 16 from Yigitcan Turna.
The Turkish club prevailed despite another double-double from FMP's center Miroslav Raduljica.
The EuroBasket 2009 silver-medal winner finished with 17 points and 10 rebounds.
Raduljica now has three double-doubles in the EuroChallenge this season.
"Before the game, both teams had already qualified for the next round. We knew that had we won this game by nine points or more, we could finish top of the group. Although we indeed held that nine points advantage on many instances during the game, our rival was right behind us throughtout. We played some good defense in the last period, and then we won the game by 11. We would like to win the game against Okapi Aalstar next week to keep first place inthe group."
Yiğitcan Turna, Banvit:
"It was a good challenge for both of teams. We had some injuries, but we covered for them with a team performance. We wanted to win this game by nine points or more and we accomplished this by working hard both during the game and in our practice session before it."