Harris also rushed for 83 yards and a score as the Blue Devils (1-1) overcame a sluggish start to win their home opener for the eighth consecutive season.
Duke scored three touchdowns in the final 3:10 of the first half, turning a 10-7 deficit into a 28-10 lead.
Harris had scoring strikes of 22 yards and 39 yards to Mateo Durant and Eli Pancol, respectively, and capped the spurt with a 6-yard touchdown run on a quarterback draw.
Jalon Calhoun had eight catches for 105 yards and two touchdowns for the Blue Devils.
Jeremiah Martin rushed for 82 yards, including a 66-yard touchdown, for N.C. A&T (1-1).
Noel Ruiz made field goals of 40 and 36 yards for the Aggies.
N.C. A&T: It’s no fluke that the Aggies, reigning champions of the Mid-Eastern Athletic Conference, beat a Football Bowl Subdivision opponent each year from 2016-18. They were stout on defense and opportunistic on offense until Duke’s flurry at the end of the first half, indicating that they can be a force again in the Football Championship Subdivision.
Duke: The Blue Devils had four penalties for 49 yards, plus another holding penalty that was declined, in the game’s first 18 minutes. It’s the kind of start they can’t afford in Atlantic Coast Conference play. But Duke settled down as Harris found his footing. Harris completed 10 of his final 11 passes of the first half, capitalizing on a variety of short throws.
N.C. A&T: The Aggies visit Charleston Southern on Sept. 14.
Duke: The Blue Devils play at Middle Tennessee State on Sept. 14.