Sherwood Brown supplied 17 points and eight rebounds for the Eagles (26-10), who became the first-ever 15th seed to make it to the regional semifinal round.
Chase Fieler helped out with 11 points and Brett Comer had 10 points and 14 assists for FGCU, which began its Cinderella story with a 78-68 triumph over No. 2 seed Georgetown.
The Eagles go on to face third-seeded Florida in Arlington, Texas, in Friday's South Regional.
Jamaal Franklin led the seventh-seeded Aztecs (23-11) with 20 points and 11 boards. Chase Tapley added 17 points for SDSU.