Hunter Hudgins recovered a fumble in the end zone for the game's first score after Pujals was stripped of the ball at the goal line. Late in the first quarter, Pujals connected on a 42-yard pass to Jake Wieczorek.
A 26-yard field goal by Connor Fitzgerald and another 3-yard touchdown pass to Flaherty capped the scoring for Holy Cross (2-2).
Pujals finished 17-of-27 passing for 177 yards and the three scores.
The Great Danes (2-3) were outgained 349-203.
Albany had won the only other meeting between the two schools with a 14-13 victory at home last season.