Bowa questioned Penny's work ethic and commitment.
Penny questioned Bowa's integrity.
But that was before Saturday, when they met privately before a 9-1 Dodgers victory.
"Me and Larry talked and it's over with," Penny said, according to the Los Angeles Daily News. "We both apologize. He wished me the best of luck and I wished him the best of luck."
Acquired last month from the Boston Red Sox in a deadline waiver deal, Penny was plagued by a shoulder injury in 2008 before leaving in the offseason as a free agent.
A two-time All-Star with the Dodgers in 2006 and '07, he was set to face his former team Sunday for the first time as a Giant.
"I never doubted he was hurt. The only thing I had a problem with was his work ethic," Bowa said Friday, according to The San Francisco Chronicle. "If you're hurting, you can still go outside and run. You can still attend meetings. You can help young kids on how to pitch certain guys. You can be on time. That's all.
"He didn't go to meetings. He didn't do anything."
The Dodgers' third-base coach confirmed Saturday the San Francisco newspaper brokered the one-on-one meeting.
"That's the last you're going to hear about it," Bowa said.
Penny was 6-9 with a 6.27 ERA in his fifth and last season with the Dodgers before going 7-8 with a 5.61 ERA this year with the Red Sox.
In two games with the Giants, a fastball that has reached 98 mph has helped him go 2-0 with a 1.20 ERA.
According to The Chronicle, Penny and Bowa separately thanked the paper's beat writer for the idea.
"Man to man," Penny told The Chronicle of the meeting. "The way it should have been."