Jamie Silva's interception ended the game as the Eagles (3-0) Tom O'Brien became the winningest head coach in school history.
The Eagles had to overcome a 436-yard passing performance by Brigham Young's John Beck.
With a first down at the BC 14, linebacker Robert Francois rushed up the middle before deflecting Beck's pass. The ball wobbled toward the turf, but Silva dove for it. The initial ruling was an incomplete pass, but after replays, the officials changed the call, ending the game.
Ryan completed 29-of-48 passes for 356 yards with two touchdowns and a pair of interceptions. Brandon Robinson caught seven passes for 140 yards and a score for Boston College.
Beck connected on 38-of-59 attempts with a touchdown and two interceptions.