Howard scored two touchdowns in the fourth quarter and then hung on to beat Morehouse 30-27 on Saturday.
The Maroon Tigers had one final shot at the win, but Howard sacked Byron Ingram as time expired.
It was the first meeting between the prestigious Historically Black Colleges and Universities schools since 1997. The win marked Howard's fourth straight over Morehouse in the 88-year rivalry between the schools.
The Bison were led by quarterback Greg McGhee, who threw for three touchdowns. He finished with 248 yards on 22 of 29 attempts.
Howard took a 30-20 lead on Charles Brice's 17-yard run with 6 minutes to play. The Maroon Tigers cut the deficit to three when Latavius Watts returned a Brice fumble 15 yards for a touchdown with 2:20 to play.
Morehouse running back David Carter finished with 127 yards on 10 carries.
Howard, in the Division I Championship subdivision, has dominated the series with the Division II Maroon Tigers, winning 11 of the last 13 games. The Bison also outscored the Maroon Tigers 127-19 in the last three matchups.
But this week's competition was marketed as "more than a game" with a focus on the scholar athletes and the intellectual rigor of both schools.
The week included numerous events ranging from a Black Male Achievement symposium on Thursday to a chapel service Sunday led by Morehouse President Dr. Robert Franklin. The symposium was designed to reaffirm the positive image of black men.
Aside from providing special events for visiting students, fans and alumni, the renewal of the series will help unify the two institutions.
"It was really good to see students from Howard and Morehouse intermingling." Mark Russell, a Morehouse alumnus from Washington, D.C., said. "After all the trash talk, we were still able to come together and reflect more on our similarities than our differences."
Howard will take on Morgan State next Saturday as Morehouse returns home to face Edward Waters College.