Juwan Staten, who finished with 12 points, made a pair of driving layups 22 seconds apart to put the Mountaineers ahead 59-52 with 2:09 left.
Bad blood between the rivals heated up late in the game.
Although no fight broke out, players from both teams had to be separated with 1:39 left after a Kilicli basket. The officials went to the replay monitor to sort things out.
Marshall's Robert Goff was ejected, as were four West Virginia players who left the bench: Aaric Murray, Terry Henderson, Jabarie Hinds and Eron Harris. One player for each team also was assessed a technical foul, and two more technicals were called in the final minute.
The annual game at the Charleston Civic Center was moved from its traditional January slot this season to accommodate West Virginia's debut in the Big 12.
West Virginia missed eight of its first nine shots and trailed by as many as seven early in the first half. Marshall started having turnover problems and lost its shooting touch after starting out strong.
Murray provided a spark with his only three baskets of the game in a two-minute span, putting in a rebound to give the Mountaineers their first lead, 25-24, with 2:45 left until halftime.
Marshall was held to one field goal over the final five minutes of the half and West Virginia finished on a 12-1 run to lead 31-25.
"What helped us lose the game was our 13 turnovers in the first half," Herrion said. "When we were behind in the second half, you just can't have empty possessions. You have to convert — and we didn't convert."