Quinnipiac erased a late nine-point deficit, closing the second half on an 11-2 run capped by an Umar Shannon three-point play with 28 seconds left to force overtime.
Ike Azotam opened the overtime period with a jumper, and Quinnipiac scored the remainder of their points from the foul line, hitting 16 of 20 to ice the game.
The Bobcats (13-8, 8-4 Mid-American) shot 47.3 percent from the field. Shannon had 21 points and Azotam had 19.
Siena (10-13, 6-6) committed a school-record 40 fouls as six players fouled out, allowing Quinnipiac to go 47 of 65 from the free-throw line. Rob Poole scored 26 points, Brett Bisping contributed 10 and Marquis Wright had 18 with 10 assists for the Saints.
Guard Naz Mitrou-Long, whose 2015-16 season ended in December due to hip problems, has been granted a hardship waiver for the coming season, Iowa State said.
As the Sooners look to life without superstar Buddy Hield and his sidekicks, it's clear their unseasoned players will need to grow up fast.
The Central Intercollegiate Athletic Association says it won't move its headquarters, its basketball tournament or other conference championships from North Carolina, despite