However, Green, who had managed the 1980 world champions, knew that Bowa didn't have many years left and demanded a young rookie third baseman named Ryne Sandberg as a part of the trade.
After retiring, Bowa was named manager of the Las Vegas Stars, the Triple-A affiliate of the San Diego Padres, for the 1986 season.
His aggressive and often angry style combined with an extremely young and inexperienced roster led to a down 1987 season in San Diego, and when higher expectations for the 1988 team (mainly engendered by those young players showing greatly improved performances in the 2nd half of the 1987 season and the 1988 spring training slate) were not met, he was fired on May 28, 1988, with an overall record of 81–127 as the club's skipper.
When Jim Fregosi was fired as Phillies manager following the 1996 season, Bowa was one of the candidates to interview for the vacant position, which ultimately went to Terry Francona.
Taking over a team that had gone 65–97 in 2000, Bowa led the club to a surprising 86–76 mark in 2001, two games behind the National League East Champion Atlanta Braves.
Torre became the seventh manager to have Bowa on his staff as third base coach, following Lee Elia, John Vukovich, Nick Leyva, Jim Fregosi, Terry Collins, and Lou Piniella.
The Dodgers won consecutive National League West titles in 2008 and 2009, but in both seasons were eliminated in five games in the NLCS by the Phillies, managed by Bowa's permanent successor in Philadelphia, Charlie Manuel.
Bowa reunited with Joe Torre and served as his bench coach for the USA team in the 2013 World Baseball Classic.
[5] Bowa returned to Major League Baseball and the Phillies by joining Ryne Sandberg's staff as bench coach for the 2014 season.
Bowa was relieved of his coaching duties on October 13, 2017, and accepted the role as Matt Klentak's senior advisor to the general manager.
He also hosted a weekly show during the baseball season with Chris Russo on Sirius XM while occasionally providing postgame analysis for Phillies games on WPHL.