Syracuse went ahead for good on a spin move by Waiters with 6:03 to play, but the lead was never more than three points.
Gasser made two free throws with 31 seconds left to bring Wisconsin within 64-63.
"I think that was the best game anybody has ever played against us and didn't beat us," Boeheim said.
The win was No. 890 overall for Boeheim, third on the all-time list, and it was his 48th in the NCAA tournament, breaking a tie for fifth place with John Wooden.
"Syracuse just has too many athletes that can do so many things, and it's hard to prepare for that on the defensive end. You think you're getting things done, but you're a step behind," Badgers coach Bo Ryan said. "So we did the best we could, and I thought we played great defense. Not everybody on the court agreed with that, but I thought we played unbelievable defense for the most part. "
Syracuse won again without starting center Fab Melo, who was declared ineligible for the tournament by the school just days before the Orange opened with a shaky win over 16th-seeded North Carolina-Asheville.
The Badgers were trying to reach the regional final for the first time since 2005.
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