The Crusaders (12-15, 7-10 Patriot League) lead throughout the second half before Franz Rassman's two free throws at 38 seconds put the Greyhounds (11-17, 7-10) on top 60-59.
Holy Cross regained the lead on Miller's first two free throws and after a Loyola miss with two seconds left, Miller grabbed the rebound and was fouled with one second left, allowing him to secure the win.
Justin Burrell added 11 points for Holy Cross, which shot 51.3 percent (20 of 39) and made 20 of 27 free throws.
Tyler Hubbard led the Greyhounds, who were 11 of 17 from the foul line, with 17 points. Rassman and Cam Gregory scored 12 points apiece.