The Matadors (16-17) shot 53.6 percent from the field and will face third-seeded Long Beach State in the semifinals Friday.
Christian Standhardinger paced Hawaii (20-11) with 28 points (14-of-16 free throws). Keith Shamburger finished with 20 points and Brandon Spearman had 17.
CS Northridge led 37-21 in the first half, but Hawaii stormed back to lead by 13 in the second. A 3-pointer by Greene with 16 seconds left forced overtime.
Shamburger hit a jumper and free throw to go up 84-81 in overtime, but two Hawaii turnovers allowed CS Northridge to move ahead as Stephen Maxwell hit a jumper and Tre Hale-Edmerson sank two free throws. Spearman couldn't connect on a 3-pointer in the final seconds.