Pogba was reportedly late for a team meeting ahead of the game against their German opponents.
Head coach Massimiliano Allegri has opted to make an example of the France World Cup winner for his tardiness.
Pogba only made his first appearance of the season against Torino on February 28 before climbing off the bench in last Sunday's 1-0 defeat at AS Roma in Serie A.
He was expected to make his first start of the campaign against Freiburg but will now have to wait for his second full debut for Juventus.
Pogba rejoined Juventus from Manchester United on a free transfer last summer but injury problems, which also forced him to miss the FIFA World Cup in Qatar, saw him sidelined until late last month.
The 29-year-old suffered a number of setbacks in his recovery before finally appearing as a substitute in the Turin derby.
The Europa League represents Juventus' best chance of making next season's Champions League after they were docked 15 points in Serie A for financial misappropriation.
Allegri's side knocked out Nantes in the previous round and will be favourites to progress against tricky Freiburg.
