Earlier this week, Pederson told Fox Sports Live with Jay & Dan that he was "a mental head case" during a home game against the Marlins in April after he approached Bonds for a picture beforehand, only to watch the former Giants slugger turn his back without comment.
The thing is, Bonds said he doesn't remember that happening.
"I got a phone call from somebody about it, and I said, 'What? I did what?' So I just called the young man up maybe 45 minutes ago, and I apologized, because that's what he felt took place," Bonds said Friday in the visitors' dugout at Turner Field, where his team is playing the Braves this weekend. "What was really funny about that situation is that I didn't even know that it happened. I don't like talking to the media about these things, but I'm telling you about the phone call and that I apologized to the kid, because I've never done anything to a ballplayer like that in my life.
"How do the young kids say it nowadays? I didn't mean to 'dis' him. So I made a point today to call him up and apologize."
"He apologized and I accept his apology. It's all good," Pederson said. "Surprised? Yeah. It was very nice of him and I appreciated the call, appreciated him reaching out to call and clear things up."
Bonds expressed to Pederson that he wished the matter could have been addressed privately.
"I told him, 'It's an unfortunate situation that you felt you had to go to the media to make that statement when, technically, it was an honest mistake, and I didn't go out of my way to do something like that, because I've never done anything like that in my life,'" Bonds said, easing into a smile. "Now if somebody told me I did that to [a reporter] or somebody like that, I might believe you on that. I've turned my back on the media and walked away, because I really didn't want to get involved in a conversation.
"But I have no reason to 'dis' another ballplayer for no reason. He's a young player. He's a good player. So it's better for me to apologize to him if there was a misunderstanding and to let him know, 'That ain't me.'"
Terence Moore is a columnist for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.