"I'm not happy, to say the least," Jones said after the Braves completed a three-game sweep of the Rockies with a 7-2 victory on Sunday.
"Any time a grown man gets his integrity questioned, they're going to take it seriously and I'm no different. If he wants to discuss it, we'll discuss it, but he's wrong, plain and simple," Jones said.
Asked by reporters earlier in the day for his side, Moyer declined to comment.
Jones was given the day off Sunday. On Saturday, he was on second base after doubling off Moyer in the fifth inning of Atlanta's 13-9 victory.
As he was engaged in some casual banter with Rockies shortstop Troy Tulowitzki, Jones said Moyer approached and said, "I see you (stealing signs)."
"It caught me by surprise," Jones said. "I was in shock. I didn't realize he was talking to me, and then I realized that he was, and I started screaming back at him. He never did turn back around."
Jones said he would be willing to discuss the matter if he gets a call from Moyer. But Jones emphasized that Moyer's allegations are meritless.
"Never have I wanted a sign when I was hitting, and I have never relayed a sign to a hitter from second base, ever," Jones said.