The sophomore quarterback threw for a touchdown and ran for another score before leaving early in the third quarter with a hip injury.
Boyd completed 16-of-26 passes for 283 yards. Freshman Cole Stoudt took over for Boyd and finished with 37 yards through the air.
Andre Ellington gained 117 yards on 22 carries and scored a touchdown for Clemson (6-0, 3-0 ACC), which jumped out to a 20-0 lead.
Chase Rettig had 129 yards on 13-of-20 passing with one touchdown and one interception for the Eagles (1-5, 0-3).