Bouknight, who played two seasons for Connecticut and is an NBA rookie, was sitting in the front row opposite the Xavier bench when he was asked to leave.
Bouknight then moved to the UConn student section.
"That was not an ideal scenario because we were playing bad and kind of melting down a bit," UConn coach Dan Hurley said. "He got tossed. I didn't really see what happened. And then I saw him again somewhere near the student section."
Playing before a raucous, sold-out crowd for the second straight game, the Huskies hit 52% of their shots and took a 17-point lead at halftime before withstanding a second-half surge from the Musketeers.
UConn is 7-0 this season in Gampel Pavilion, its on-campus arena.
Information from The Associated Press was used in this report.