With a runner on first and one out and the Cubs trailing, 3-1, Reds right-hander Mike Leake threw a 1-1 fastball to Clevenger, who took the outside pitch, which was ruled a strike by Nelson.
Clevenger -- who also appeared to be upset when he was called out looking in the second inning -- argued with Nelson before being ejected.
"I think the first pitch, obviously, he wasn't happy with," Cubs manager Dale Sveum said. "He's got to have a little more composure than that when he's a catcher. You can't be getting thrown out of games like that for situations like that."
Welington Castillo replaced Clevenger and proceeded to strike out swinging. The strikeout was charged to Clevenger.