Duke redshirt freshman running back Brittain Brown rushed for 120 yards on 10 carries, scoring one touchdown.
Duke led 40-0 with nearly eight minutes left in the second quarter. The final score marked the first time a David Cutcliffe-coached team reached the 60-point mark.
Duke cornerback Bryon Fields Jr. returned an interception 28 yards for a touchdown.
Jones' passing touchdowns went to Aaron Young on a 54-yard play and Johnathan Lloyd on a 24-yard play. Young caught five passes for 89 yards.
Jones finished 19-for-25 for 213 yards. Thirteen Duke players made at least one reception.
The scoring opened on running back Shaun Wilson's 1-yard run. Fields had the interception return on the next play from scrimmage.
It was an impressive beginning to the season for the Blue Devils, who were coming off a 4-8 season. Duke racked up 281 passing yards and 243 rushing yards.
Duke improved to 6-0 all-time against its cross-city opponent, which plays as a member of the Football Championship Subdivision. The Eagles are the three-time defending Mid-Eastern Athletic Association champions.
It was the first of four home games this month for the Blue Devils.
N.C. Central freshman running back Isaiah Totten burst away for an 81-yard touchdown run in the second quarter.