Murphy scored three minutes into the game off a corner, but Great Valley was unable to convert on any of its other opportunities.
"I think they found their form to get back in the game and we took the pedal off the gas after the first goal," Murphy said.
With five minutes remaining in regulation, a Great Valley defender knocked down a shot in the box and the referees ruled he played it with his hand.
On the ensuing penalty kick, Nate Delgado found the lower left corner of the net for the tying goal.
"To me, it looked like his hands were by his body and the ball hit around his waist," Great Valley coach Dave Moffett said.
"I thought it was a poor call."
Conestoga Valley (23-2-2) took advantage of a corner in overtime, when Whitacre scored with 2 minutes, 11 seconds left in the first overtime to win the game.
While Great Valley (24-1) came up short, it was able to reflect on a successful season.
"There were so many magical memories and so many great games," Moffett said. "The luck tonight just didn't go our way."
"This is the best team I ever played for. We're going to look back on this and have a lot of great memories," said Murphy, a senior. "They're great people and better players. I'll tell them to keep their heads up and look forward to next season."
Conestoga Valley 0 1 1 – 2
Great Valley 1 0 0 – 1
Goals: CV-Nate Delgado, Connor Whitacre; GV-Patrick Murphy.
Saves: CV-Zachary Rider 2; GV-Jon Fuydal 3.