The 49ers (7-5) put the game away with a 16-0 run for a 62-38 lead with 3:26 remaining. Ware scored eight points during the spurt, including a pair of 3-pointers. Auburn (8-2) went more than nine minutes between field goals.
Long Beach State will play Kansas State in Sunday's final.
T.J. Robinson grabbed nine rebounds and Phelps had eight as the 49ers held a 43-25 advantage on the boards.
Auburn finished 15 of 57 from the field. The Tigers' only threat was Frankie Sullivan, who finished with 22 points on 8 of 16 shooting.