Coach Kyle Whittingham made the announcement Monday but did not elaborate on the injury.
The third-ranked Utes (6-0), the last undefeated team in the Pac-12, play at USC on Saturday.
Fakailoatonga started the last five games after Evan Moeai was lost for season in the opener. He had 12 receptions for 120 yards, ranking fourth on the team in both categories.
Sophomore Harrison Handley moves to the top of the depth chart and freshman Caleb Repp is listed as the backup. Handley has two touchdowns on nine receptions this season.