Lee threw three touchdown passes in the first half, two to Dominique Taylor and one to Rashard Davis, to help the Dukes to a 24-17 edge at halftime.
Maglio kicked his second field goal to cap the first drive of the second half, making it 27-17. Following a Towson score that closed the gap to 27-23, Charles Tutt returned the kickoff 92 yards for another Dukes touchdown. Lee connected with Brandon Ravenel on the team's next possession for a 29-yard score, giving James Madison a 41-23 advantage with 2:34 left in the third quarter.
Connor Frazier had 176 yards passing with three touchdowns for the Tigers (2-3, 0-2).