In the top of the fourth inning, Clemens attempted to lay down a bunt to move Alexei Ramirez over to second base. The pitch from Jake Thompson was up and inside, and Clemens managed to make contact and get the bunt down.
However, he took exception to the pitch location, threw his bat into the ground in frustration, and didn't run down the line to first. Double play. Inning over.
"When I took him out of the game, when I went on the mound I basically said to him, 'No way is anybody giving up on you, but there's things that aren't going to happen in Padre uniforms,'" said Padres manager Andy Green. "To me, throwing a bat, not running to first base after a bunt -- it's not going to happen."
Green let Clemens back on the mound for one out in the fifth inning only so that left-handed reliever Buddy Baumann -- who would go on to pick up his first Major League win -- could get warmed up.
For Green, pulling Clemens was about making sure something like this didn't happen again, in addition to a few other "minor things" that Clemens did that bothered him during the game.
"I came up between innings and talked to him," Green said. "'There's literally no hard feelings, I'm not upset with you. We're going to get this right. We're going to get it right as a team.'
"I think he is a guy that wants to do things right. I think he gets the message and he's excited about his next turn in the rotation. … I think he just kind of lost sight of context of the game and what he needed to do. There's nothing malicious in him at all. It's just, we're going to remember in the future. It's as simple as that."
Clemens, for his part, admitted that Green was right to take him out of the game, and said that the pitch from Thompson took him out of the situation on the field.
"You know, just a lack of cerebral-ness right there," Clemens said. "Being in the moment, I was thinking more about the pitcher and what he did than I was about the fact that you have to get down the line pretty quickly with a bunt that's straight back to the pitcher.
"So I think I was just more concerned with what just transpired between me and the pitcher, moreso than the game."
The former Miami pitcher said that he has the utmost respect for Green, and that he would learn from the situation and move on.
"Me and the skipper have been on the same page since I've been here," Clemens said. "I think he likes what I bring to the table and, you know, I love being here. Just gotta clean up a few things, not get so frustrated with the pitcher right there and stay in my tunnel vision."
When asked if this was a fineable offense, Green said that he had no desire to take money from players, and that he'd never done that at any point in his career.
"I don't want to make more of a deal than it is," Green said. "This, to me, is a dead issue that he's going to understand well going forward. … There's nobody in our clubhouse that's upset going forward. He was back on the bench cheering on his teammates; very much a part of the team.
"It wasn't like, 'ostracize this guy for doing something wrong.' We all make mistakes. We dealt with it in a very forthright fashion, and move on."
Carlos Collazo is a reporter for MLB.com based in San Diego. Follow him on Twitter @CarlosACollazo. This story was not subject to the approval of Major League Baseball or its clubs.