Dungey looked like he was going to get the second half off after the Orange built a 34-7 lead, but he returned after Western Michigan made it a six-point game in the third quarter.
Dungey lobbied coach Dino Babers to get back in and put the game away upon his return.
"I love to win and want to do everything I can to win," Dungey said. "Once I could see that it was starting to get close, I was in Babers' ears. He was probably getting annoyed with me, but I really wanted to get back in there."
Dungey connected with Jamal Custis six times for 168 yards and two touchdowns, all career highs for the senior wide receiver.
Syracuse scored the first 17 points, and converted its first six possessions for points before the Broncos mounted a comeback, scoring 21 unanswered to start the second half until Dungey's return.
Western Michigan quarterback Jon Wassink was 19-of-36 passing for 379 yards, three touchdowns and two interceptions.
Wassink threw two touchdowns to D'Wayne Eskridge, including an 84-yard score to make it 34-21 with 7:32 left in the third quarter. Eskridge caught eight passes for 248 yards.
LeVante Bellamy had a 64-yard run to make it 34-28 before Dungey's return put Syracuse back on track.
"I'm not going to say the word frustrated, but I was disappointed," Babers said. "But the fortitude that they turned around with and how they took over the fourth quarter when we put our four fingers up and it's all about us and our conditioning. For them to go out and take that game back, take any hope that those guys had at winning the game in the fourth quarter. I'm really proud how they battled back."
Syracuse: Dungey proved he's one of the top dual-threat quarterbacks in the country, and the Orange defense was good early. After the quarterback missed the final three games last season — and the defense gave up 54.0 points per game in that stretch — the first half gave fans reason to believe after dropping five straight to finish 4-8 last year.
Western Michigan: The Broncos were pummeled early on but rallied. But despite losing their 13th season opener in 14 years, Western Michigan has reached a bowl game in six of those seasons. Western Michigan will have another shot at Syracuse in 2019 at the Carrier Dome.
Syracuse: The Orange host FCS program Wagner in its home opener on Sept. 8.
Western Michigan: The Broncos play at No. 14 Michigan on Sept. 8. Western Michigan is winless in six games against the Wolverines.