West Virginia (30-23) chased Marshall starter Alex Thackston with a three-run second, but five Herd relievers combined for eight innings of onerun baseball.
Ryan Hopkins (4-2) got the win after facing just one batter, relieving Michael Taylor with a runner on second in the seventh. Matt Hummel threw a perfect eighth and Josh King did the same in the ninth for his team-leading sixth save.
"It wasn't actually their bullpen. They ran their weekend starters out there," firstyear WVU Coach Randy Mazey said. "But that's what they do. Their weekend starters always pitch against us, and they pitched better than we did."
Taylor and Chase Boster, who replaced Thackston in the second, have weekend starting experience, but Waggoner said the pitchers he used will be sent to the bullpen for the regular season-ending series at Rice that starts Thursday.
"They did a great job of coming in and keeping us right there in the game," Waggoner said.
Mazey elected not to play several of his starters, including outfielders Jacob Rice, who is hitting .327, and Brady Wilson and catcher Alan Filauro. WVU plays its home Big 12 series at Appalachian Power Park, and Mazey was concerned fatigue is setting in.
"Travel has been a problem all season, and I thought last week that maybe it started to wear on us a little bit," Mazey said. "In the interest of trying to win our conference, we went with rest. Not saying that's why we didn't win the game. But, yeah, we only brought about 10 (position) players and five pitchers on the trip."
The lesser-used players made their presence known.
Chris Rasky, an .087 hitter going in, got the Mountaineers' three-run second inning started when he singled to right, then went to second on a throwing error by Stafford. After Constantini walked, catcher Max Nogay bunted to the left side of the infield. Thackston tried to force Rasky at third but was late with the throw.
Kevin Cohen was hit by a pitch to drive in Rasky. Billy Fleming ran a 2-0 count on Thackston before Waggoner brought in Boster. Fleming then doubled to drive in Constantini and Nogay for a 4-1 lead, but Cohen was gunned down at third.
Each team scored single runs in their half of the first. Marshall got a run in the third and another in the fifth to pull to within 4-3.
WVU got a run in the seventh when Ryan McBroom singled and scored on Rasky's two-out double.
Harlow (0-2) took the loss. He gave up all three Herd runs in the seventh and allowed three hits in 12/ 3 innings.
The Mountaineers, tied for second in the Big 12, start a three-game series at Oklahoma State on Thursday. Marshall will go to Rice clinging to a one-game lead over UAB for the eighth spot in the Conference USA standings.