Dayes also scored on runs of 2 and 8 yards, and Shadrach Thornton added TD runs of 39 and 4 yards for the unbeaten Wolfpack (4-0).
Jacoby Brissett tossed TD passes of 33 and 2 yards to Jaylen Samuels, and the Wolfpack defense intercepted Jags quarterback Cody Clements twice as N.C. State opened up a 42-10 halftime lead.
Reggie Gallaspy II capped the Wolfpack scoring with TD runs of 12 and 10 yards.
The Jaguars (2-2) of the Sun Belt Conference scored on an 11-yard TD pass from Clements to Gerald Everett and Aleem Sunanon added field goals of 33 and 49 yards.
The crowd of 21,314 got worked up early when South Alabama went 75 yards in six plays on the game's opening possession, capped by Clements' 11-yard TD pass to Everett with just 1:53 gone.
But the Wolfpack answered when Dayes bolted down the right sideline in front of his bench for the 77-yard score on their third play from scrimmage.
Thornton's TD made it 14-7 and after a Germaine Pratt interception at the at the Jaguars' 23 the Wolfpack went 77 yards in one minute, capped by Dayes' two-yard TD run.
Suddenly, the reality of an impending beat-down had the home crowd sitting on its hands.
Jerod Fernandez picked off Clements again and returned to the USA 8, and Dayes ran in from there for his third TD of the evening and a 28-7 lead.
A pass interference penalty against N.C. State in the end zone late in the quarter set up USA with a first and goal at the 6. But three plays lost five yards and they had to settle for Sunanon's 33-yard field goal on the second play of the second quarter.
Jacoby Brissett two scoring passes to Samuels made it 42-10.
Thornton's second TD of the game made it 49-10 midway the third quarter, before Gallaspy's two scores capped the night.
Sunanon's career long 49-yarder capped the scoring for the Jaguars.