The 19-year-old power forward from Serbia, fresh off a 27-point game-winning performance over CSKA Moscow, drilled a three-ball with just 28 seconds remaining as MKB beat Gambrinus 76-73.
Brno, beaten finalists in last year's EuroLeague Women, had a chance to force overtime but Hana Horakova and Tamika Whitmore each missed shots from the arc before time expired.
Milovanovic finished with 21 points, including 14 in the fourth quarter.
The outcome means MKB have leapfrogged CSKA into second place, and home court advantage in the Eighth-Finals while at the same time complicating CSKA's path to the Quarter-Finals.
Gambrinus, meanwhile, finished 4-6 and they will now face an xtremely difficult Eighth-Finals tie.
The Czech giants led by 10 seven minutes into the second quarter but went to half-time only with a 42-38 advantage.
Milovanovic had just three points at the break.
The game remained tight with Gambrinus taking a 58-55 advantage to the final quarter.
Whitmore opened the final frame with a three, but Dóra Horti made two free throws and Milovanovic started to heat up with a three-pointer.
MKB's crowning blows came after Hamchetou Maiga-Ba's jump shot had put the home side in front at 73-70.
Amber Holt nailed a three with 1:40 remaining to tie the game.
After Brno's Timea Ivkovicné Béres missed two free throws, MKB's Kathleen MacLeod launched a long-range shot but was off target.
Hana Horakova rebounded but Katalin Honti stole the ball soon after from Whitmore.
That set up Milovanovic who hit the game-winning three.
Gambrinus made just 17 of 26 free throws compared to an impressive 26 of 32 effort for MKB.