The vote broke a trend some commissioners called a "gentlemen's agreement" that has maintained a black mayor pro tem since the position was created during consolidation.
Commissioner Corey Johnson, who also was nominated for the No. 2 post, was the sole no vote. Commissioner J.R. Hatney, who nominated Johnson, abstained.
After the vote, Hatney motioned for the commission to give its unanimous support to Bowles. Commissioners voted 10-0 in favor.
Mayor Deke Copenhaver said the motion for unanimous support "sends the right message."
Bowles said he appreciated the gesture, which was not afforded his predecessor, Commissioner Alvin Mason.
The election was one of a handful of actions taken during the first commission meeting of 2011.
Before the meeting, Johnson, Copenhaver, commissioners Joe Jackson and Mason, and new commissioners Grady Smith and Wayne Guilfoyle were administered their oaths of office.
Elected in November, all voiced appreciation to their wives and families, their fellow commissioners, voters and God for the privilege of serving in city government.
Johnson called his re-election a "defining moment," while Copenhaver said he looked forward to working with men he considered "friends as well as colleagues."
Copenhaver's pastor, the Rev. Leslie Holmes, of Reid Memorial Presbyterian Church, gave the opening prayer at the meeting, asking that the mayor "govern for the good of all, and may Augusta become a model city for others."
In attendance at the swearing-in ceremony was four-time Purple Heart recipient Master Sgt. Michael Morton, to whom Jackson last year donated his Masters badges, a commissioner perk.
"Since then, we've become close family friends," Morton said.
Also present was former Fort Gordon commander Jeff Foley, who helped Mason, a federal employee at the base, obtain permission to run for elected office.
Mason "does a great job, and we're very proud," Foley said.
Augusta District 8 Commissioner Wayne Guilfoyle is sworn in. Several others were sworn in during a ceremony Tuesday. Commissioners then voted for Joe Bowles to assume the No. 2 position of mayor pro tempore.