Endres was suspended for a pattern of violations of the school's substance abuse policies, a source told ESPN's Joe Schad on Wednesday.
Endres was suspended during the preseason and missed the team's first three games this season. He relieved starter Zach Frazer near halftime against Buffalo on Sept. 25 and started the team's next two games.
Endres, a junior, completed 60 percent of his passes for 471 yards and five touchdowns with two interceptions while going 1-1 as a starter.
UConn said he will miss the entire 2010-11 academic year.
The news came a day after coach Randy Edsall announced that starting offensive guard Erik Kuraczea had withdrawn from the school. The sophomore was suspended with Endres in August, and returned with him in September. He started the last two games at left guard.
The school would not say if Endres' violation and Kuraczea's departure are linked.
At the team's weekly media luncheon on Tuesday, Edsall said Kuraczea was leaving for "personal reasons" and Endres expressed surprise.
"It's tough because he's a good player, and I really enjoyed playing with him," Endres said. "It's disappointing to me."
Edsall is expected to address the situation during a conference call with reporters on Thursday.
Brian Bennett covers Big East football for ESPN.com. Information from The Associated Press was used in this report.