Juventus had the lead for the majority of the first half, but Prienai jumped in front 39-37 with a three-pointer by Mindaugas Lukauskis to close the second quarter.
However, the hosts took back the initiative into their hands in the second half, gaining a 59-50 edge after a 10-2 run in the third quarter.
With around five minutes left in the game, Juventus still had a 78-67 advantage, but Laimonas Kisielius dropped in a couple of three-pointers to spark an 8-0 run to bring Prienai back in the game.
With 1:16 left to play, Gintaras Kadziulis cut the gap to three points and then made it a one-point game in the next possession.
Juventus still had an 82-81 advantage and the possession of the ball with 29 seconds to play, but Aidas Viskontas turned the ball over. Prienai made sure to cash in, with Arturas Valeika making the game-winning basket with almost no time to spare.
Laimonas Kisielius had a game-high 23 points on 5-of-8 shooting from downtown, Gintaras Kadziulis scored 18 points, while Arturas Valeika chipped in with 14 points and eight rebounds for the winners.
For Juventus, Saulius Kulvietis had an excellent game, finishing the evening with 22 points and eight boards, Nikita Barinov collected 14 points, as Aidas Viskontas had 13 points.