In the process, Adam Weistling walked and Waynesboro manager Greg Chandler instructed Arendt to issue an intentional walk to Josh Crunkleton.
With Clint Castellar at the plate with a 2-0 count, the home plate umpire hurried from his position to signal a balk on Arendt, alleging Arendt dragged his foot off the pitcher's mound with a motion toward home plate before stopping his delivery.
While Chandler vehemently argued, Kopp crossed home plate with the winning run, sending the No. 1 Indians (4-3) to their third straight loss in 24 hours, which included a loss earlier Saturday to Gettysburg.
"The (plate umpire) said the pitcher drug his foot forward," Chandler said. "This was a big rivalry game and I've never seen anything like this with all the indecision, and hope I never see another one like it."
Greencastle coach Chris Sellers was obviously pleased with the victory that elevated the Blue Devils' record to 6-2, but was not particularly pleased with the intensity of his team.
"We'll take the win ... it's a shame the game couldn't have been decided on a hit," Sellers said. "We didn't have much intensity today. Maybe it was because of three games in a row."
Greencastle drew first blood in the opening inning on a mammoth one-out, two-run homer to left by Brett Sellers that brought in Brett Hoffman, who had walked.
Arendt settled down and retired 11 Blue Devils in a row and enabled his teammates to forge a 3-2 lead.
After a walk and stolen base by Seth Livengood to open the second, Sean Hyndman drilled a single to center.
A two-run fourth inning on singles by Derek Shafer and Corey Livengood wrapped around a triple by Hyndman put the Indians on top, 3-2.
At that point, Chandler brought in Brett Thrush to pitch and he quelled Waynesboro bats for the final 3 2/3 innings allowing only one hit.
"This was the first Thrush has pitched in two weeks," Chandler said. "He was throwing his forkball for strikes and outs. He was terrific."
Greencastle tied the game 3-3 in the last of the fifth when Arendt threw wildly to first on a pickoff attempt of Castellar, allowing Crunkleton to score.
It might have been a Greencastle lead earlier in the inning, but a perfect strike by Josh Mummert from left field erased Adam Weistling, who tried to score on Crunkleton's single.