The ejection occurred after David Ross' check-swing was ruled ball four with the count full. First-base umpire John Hirschbeck ruled Ross didn't offer at Carter Capps' pitch.
Miami hasn't had many appeals go its way this season, and Jennings decided to speak his mind, drawing an immediate ejection.
"The umpires are paid to do a job," Jennings said. "Every manager, every player has a certain point. But this isn't about me. That was my reaction, but this is about the team. These guys rallied. They picked each other up. This was big."
Jennings replaced Mike Redmond, who was dismissed on May 17. In his 16th game, the team's new skipper, who transitioned from being general manager to the dugout, was tossed for the first time.
"That's not the story," Jennings said. "I want to focus on the team."
Jennings, who never coached or managed at the professional level, was asked when the last time he was ejected.
"My wife," he quipped. "Every day she throws me out."
Jennings entertained his players with his emotional outburst.
"D.J. has got it in him," said first baseman Jeff Baker, who homered on Wednesday. "I like it. Let him get that first one out of the way. I don't think he's going to like the fine too much, but it was really cool."
Dan Haren, the winning pitcher on Wednesday, felt the feistiness of the night may energize the Marlins.
"Sometimes that's what a team needs -- bench-clearing and a manager being thrown out," Haren said. "It's probably a tough spot for him, because he's never gotten tossed before. It was impressive. He did a good job."
Joe Frisaro is a reporter for MLB.com. He writes a blog, called The Fish Pond. Follow him on Twitter @JoeFrisaro and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.