The Serie A side were taken to pieces by Thomas Tuchel's Chelsea midweek in the Champions League, with the Blues scoring three times in the second half for an easy win.
Juve may have had an excuse as they had already qualified for the knockout stages of the competition, but they didn't have such a let off in defeat against Atalanta, and felt the wrath from their fans.
A wayward Alvaro Morata pass was intercepted by Berat Djimsiti in the 28th minute, with the Albanian defender instantly firing a first time pass through to Duvan Zapata.
Played onside by an out-of-position Matthijs de Ligt, Zapata latched onto the ball, blasting it over a helpless Wojciech Szczesny for the game's eventual winner.
Juve left the pitch at half time to loud boos, and things only got worse in the second 45 when two of their better performers this season, Federico Chiesa and Weston McKennie, went off injured.
Atalanta closed out their first win away against Juve since 1989, leaving the Old Lady seven points from the Champions League spots in eighth place.
Allegri returned to coach Juventus this season after five Serie A titles at the helm between 2014 and 2019, and had already unleashed his fury after a poor start to the season.
This time his ire was pointed at the fourth official as the livid 54-year-old left the pitch, with the tension continuing on it.
A minor skirmish broke out between the two squads after the final whistle, while only five players in black and white had the courage to face supporters.
Fans in the Curva Sud were said to have shouted 'show some balls' throughout the match, and only de Ligt, Szczesny, Paulo Dybala, Leonardo Bonucci and Juan Cuadrado bothered to walk over and applaud them following the defeat.
Juventus sold record signing Cristiano Ronaldo to Manchester United in the summer for £12.86million, and appear to be severely lacking his goals.
The team have scored just 18 times in 14 Serie A games, the eighth worst record in the division, with Paulo Dybala their top scorer on three goals.
Allegri's side have a far easier run of fixtures on the horizon featuring all of the bottom three in their next five matches, but they could drop 14 points off of league leaders Napoli who face Lazio next.