Cunningham entered after Liggins was benched after losing his composure, according to Howard spokesman Edward Hill. The freshman completed 10-of-11 passes for 132 yards and his 13-yard strike to David Wilson gave Howard the lead, 30-29, with 22 seconds remaining.
William Parker and Aquanius Freeman paced the Howard ground game with 64 yards apiece. Freeman's 2-yard touchdown run gave the Bison a 24-23 advantage late in the fourth quarter.
Donnay Ragland led Morehouse with 238 yards through the air but was sacked four times.
Morehouse and Howard faced off for just the second time since 1923.