Smith had 161 yards passing for the Crimson (4-1). Devin Darrington ran for 109 yards and a score on 28 carries.
Holy Cross' Domenic Cozier ran 66 yards for a touchdown on the third play of the game but Smith answered quickly for Harvard with an 18-yard scoring pass to Jack Cook to even it up. Jake McIntyre booted a 36-yard field goal late in the first quarter, and Smith followed with a 22-yard touchdown throw to Ryan Reagan for a 17-7 lead.
Darrington's 3-yard scoring run early in the otherwise scoreless second quarter gave the Crimson a 24-7 advantage at halftime.
Holy Cross closed to 24-14 early in the third but Smith's 68-yard scoring strike to Cody Chrest pushed Harvard's lead to 31-14 by the end of the quarter.
Cozier ran for 98 yards and two touchdowns for the Crusaders (3-4). Connor Degenhardt had 206 yards and a score passing.
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