Dixon, who was 19-for-31 with 201 yards, gave the Dukes (2-3, 1-1 Northeast Conference) a 7-0 lead when he connected with Dave Williams for a 7-yard score with 10:36 left for the first of four straight touchdowns by Duquesne.
The Dukes took a 27-0 lead into the third quarter before the Jeff Sinclair threw a 19-yard touchdown pass to Shadrae King with 7:09 left in the period for the Colonials (0-5, 0-2).
The Dukes' running game was led by Larry McCoy with 107 yards and two touchdowns on 20 caries.
Sinclair finished with 219 yards on 20-for-36 passing with two touchdowns and two interceptions for Robert Morris.
Myles Russ ran for 85 yards on 21 carries for the Colonials.