Geno Smith was 36 of 54 for 364 yards and two touchdowns for the Mountaineers (5-4, 2-4), who gave up 55 points for the second time in three weeks. Stedman Bailey caught 14 of Smith's passes for 225 yards and a score.
Stewart had 13 catches, including touchdowns of 21 and 20 yards. He also scored on a 46-yard run.
The game marked the return of West Virginia coach Dana Holgorsen, who was the Cowboys' offensive coordinator before taking the job in Morgantown.
Oklahoma State only led 38-34 with 5:20 left in the third quarter after Smith scored on a 1-yard sneak one play after linebacker Terrence Garvin snagged a deflected pass and returned it 42 yards. But the Cowboys got a field goal and two touchdowns on their next three possessions to make the score 55-34 with just under 10 minutes left in the game. Chelf hit Stewart on a 20-yard TD, and Jeremy Smith scored on a 21-yard run. Jeremy Smith's touchdown came three plays after the Cowboys had stopped West Virginia on a fourth-and-6 at the Mountaineer's 39-yard line. Oklahoma State's defense produced a big stop in the second quarter as well, stuffing Shawne Alston on fourth-and-goal from the 2 with the Cowboys holding a 21-7 lead. Joseph Randle ran for 81 yards to go over the 1,000-yard mark, the sixth straight year an Oklahoma State back has done so. The Cowboys led 28-7 after a first quarter filled with big plays. Stewart took a reverse handoff around the right side and went 46 yards for a touchdown on Oklahoma State's first drive. Later, he made a diving catch for a 19-yard gain on third-and-2 to keep a drive alive, and finished the drive with a 21-yard TD reception and a 14-0 lead.
West Virginia's first touchdown came not on a pass by Smith, but by backup Paul Millard, who came on after Smith had his helmet knocked off on a sack that left the Mountaineers facing fourth-and-13 at the Oklahoma State 37. Millard was given plenty of time and found Bailey in the end zone to make it 14-7.
Josh Gilbert brought the crowd back to life on the next kickoff by returning it 96 yards for a TD- his school-record fifth kick return for a touchdown.
Smith threw a 17-yard touchdown pass to Tavon Austin in the second quarter to get the Mountaineers within 21-14. But the Cowboys answered with a 48-yard touchdown pass from Chelf to Blake Jackson and, after a muffed kick return by West Virginia, a short field goal to push out to a 31-14 lead.