The second-seeded Greyhounds (23-8) will face the fourth seed, Fairfield, on Monday.
Loyola shot 50.9 percent from the field (27 of 53), making 7 of 13 3-pointers against the Saints (14-17).
Shane Walker and Robert Olson added 12 points each, and Justin Drummond chipped in 10 points for the Greyhounds.
Loyola trailed 16-9 with 10:49 left in the first half and went on a 13-2 run to take the lead for good.
The Saints were led by Kyle Downey with 17 points and Owen Wright with 16. OD Anosike added 13 points for Siena, which played its quarterfinal game a little less than 16 hours earlier, defeating Manhattan 84-82 in an overtime game that ended at 12:36 a.m. Sunday.