Johnson set a career-high for yards as he rushed for 265 on 17 carries, with touchdown runs of 85 and 80 yards. Marcus Marshall had 10 carries for 94 yards, including a 70-yard touchdown to close out JMU's scoring in the fourth quarter.
Overall, ECU was outgained 614-372, with the Dukes rushing for 422 yards.
"I tell you what, you get outgained 600 yards-plus to 350 yards-plus, and you look at the score sheet and you see time of possession is the same, and you see you ran more plays than the other team, it lets you know you weren't doing anything with the ball when you had the ball," second-year head coach Scottie Montgomery said. "That's what happened. I thought our offense didn't give our defense any energy in the first half. The defense I felt like wore a little bit at the end once they continued to put up points on the board. If you play like that together, you end up losing the football game the way that we lost.
"I'm very, very disappointed, as disappointed as I've been since I've been here."
JMU led 7-0 at halftime, but quickly went 14 points ahead on the first play of the second half as Johnson went off tackle on the right side and got past the defense for an 85-yard touchdown run. It was a career-long for the senior.
Gardner Minshew started at quarterback for the Pirates and played most of the first half, with Thomas Sirk getting in for two plays on ECU's second possession. Minshew was 7-for-18 for 82 yards with one interception. Montgomery then made the decision to go with Sirk in the second half.
"This is just something I've been planning on, just waiting for my opportunity," said Sirk, who finished 21-for-35 for 210 yards with two interceptions. "I didn't know when my opportunity would come. I didn't know when they'd call my number, but I didn't ever want to be they guy who, when they called my number I wasn't prepared. So, I prepared all week just like I was going to get my opportunity. I went out there and did what I could to try to spark something for the team, try to keep us in it."
Indeed, the offense did produce more in the second half after totaling just 114 yards before halftime. On Sirk's first drive, ECU started from its own 22 and advanced to the JMU 15 before Sirk was intercepted by Rashad Robinson in the end zone.
On the next play, JMU's Bryan Schor was intercepted by Bobby Fulp on a tipped pass at the Dukes' 22-yard line. It was Fulp's third career interception.
The Pirates needed just three plays to get on the board on a 6-yard run by Darius Pinnix. After Pinnix gained four yards on the first play, Sirk threw to Jimmy Williams in the end zone, but JMU's Jimmy Moreland was called for pass interference, giving ECU the ball at the 6. Pinnix scored on the next play.
The Dukes were penalized 14 times for 172 yards, with many of those penalties for pass interference in the second half. But the penalties seemed to actually benefit them.
"They stopped a lot of big-time plays with their pass interference," Montgomery said.
ECU looked to gain more life on the ensuing possession, as Devon Sutton forced and recovered a fumble by JMU's Nick Carlton after a 10-yard pass from Schor to the Pirates' 41. But ECU was unable to take advantage as the drive ended on a fumble after a bobbled snap on fourth-and-2 from the JMU 33.
"Our biggest issue tonight is we didn't play well on the offensive front at all," Montgomery said. "It kind of started right from the get-go. We put more balls on the ground snapping the ball than I've ever been a part of. That led right into our quarterback play offensively. It wasn't very good. We didn't do the things that we were supposed to do with the football. A lot of situations we rolled opposite of the route, we got flushed out of the pocket.
"A lot of times we got into some long situations. Our receivers bailed us out a few times with their talent, but all in all we didn't do what we needed to do. I didn't think we ran the ball effectively at all. As hard as we worked on rushing, we didn't do a good job. I thought that Thomas, when he came in, he gave us a big boost, a little bit of energy. He tried to will us to scoring some touchdown drives."
The Dukes then went 64 yards on 10 plays on their next possession and went up 21-7 on a 17-yard pass from Schor to Carlton.
The Pirates drove to the JMU 20 on their next possession, which ended on a fourth-and-9 when Sirk's throw to the end zone was just out of reach of Williams.
Johnson scored on an 80-yard run on the next play, and though they missed the point after, JMU led 27-7 with 11:48 remaining.
"I think we stressed our defense a little bit by trying to ask them to go for turnovers and to put the pressure on their offense, because we weren't doing anything on offense ourselves," Montgomery said. "They felt the pressure of trying to make plays the whole second half because we couldn't move the ball, or we were moving the ball but couldn't score. "
Marshall scored on a 70-yard run with 2:34 left before Derrell Scott got ECU on the board with a 1-yard touchdown run with 23 seconds to go. Scott led the Pirates with 47 yards rushing on 12 carries.
"I'm clearly disappointed in the way we performed today, especially with the kind of camp we've had, the kind of spring we've had," Montgomery said. "Give a lot of credit to JMU, they played well offensively and defensively."
Despite dominating most of the first half, JMU held just a 7-0 lead at halftime. The Dukes outgained the Pirates 228-114, had 13 first downs to ECU's seven, and ran nine more plays. ECU hadn't been shut out in the first half at home since Sept. 14, 2007, when it trailed Southern Miss 14-0 en route to a 28-21 loss.
JMU threatened on its first drive, but that possession ended on an overthrow by Schor on fourth-and-8 from the ECU 32. But after a second three-and-out by the Pirates, the Dukes went 82 yards on nine plays, with Schor scoring on a 4-yard keeper around the right end with 5:11 left in the first quarter.
Minshew was intercepted by Jordan Brown at the ECU 40 on the first play after the kickoff. The Dukes were moving the ball again before the Pirates stopped them on second-and-1 and third-and-1 from the 19. JMU's Tyler Gray then hit the right upright on a 35-yard field-goal attempt.
The Pirates' only true scoring opportunity of the first half came on their fifth possession. Starting on their own 17, they drove as deep at the JMU 29, but had to settle for a 51-yard field-goal attempt by Jake Verity. The kick had plenty of distance, but sailed wide right.
"Defensively, I thought we found our groove in the second quarter," Montgomery said. "We found a way to kind of contain what they were doing. We made some more adjustments going in at halftime. We didn't play well at the linebacker position, at our weak-side linebacker position in this game. We lost the gap, we didn't carry some seams. It's not necessarily one person or two people, it's the entire scheme, the entire defense."
The Dukes, whose only other game against an American Athletic Conference team was two years ago (48-45 win over SMU), have experienced some success against FBS teams, including a 21-16 win at Virginia Tech in 2010. They are now 3-8 in their last 11 against FBS teams.