"I just felt like we needed a new voice," said General Manager Ed Wade. "It wasn't the easiest decision."
Gary Varsho was named manager for the final two games of the season.
Wade said there is no timetable for finding a manager for the 2005 campaign.
"We've got some names in mind," said Wade. The appropriate thing to do is to use our time to pursue them."
The Phillies entered Saturday's action with a record of 85-75, good enough for second place in the National League East but 10 games behind division champion Atlanta.
Bowa, 57, was named the 49th manager in team history on Nov. 1, 2000. Only once in his four years the team finished with a losing mark -- 80-81 in 2002.