Of 60,418 votes cast, 31,355 were in favor of the flag tail design announced by American's former top management in January 2013. A total of 29,063 voted for American's traditional AA-with-an-eagle logo for the paint job on the planes.
Employees had until noon Thursday to vote.
Parker said he didn't care "which option we chose" but added, "I'm really pleased to have a firm decision we can all embrace."
For those who wanted to bring back the old AA/eagle logo, "know that it will still be with us," Parker said.
"First, it will take us many months to paint the 580 US Airways aircraft, and those aircraft will be the priority." The remaining 539 "classic Silverbirds will still be flying for some time," Parker said.
The new American - which will be the dominant airline in Philadelphia - will continue the tradition of keeping a few vintage designs on aircraft, including those of predecessor companies PSA Airlines, TWA, and the heritage American polished-silver design.
So the AA and the eagle "will remain in our system even after all the fleet has been painted," Parker said.
Of the more than 1,100 planes to be painted, 300 are US Airways "mainline" aircraft, 280 are US Airways Express planes, and 539 are American planes.
These numbers do not include "retiring" aircraft or new airplane deliveries, the memo said.
"This was a small but important step in bringing us together and beginning to move forward," Parker said. "Now let's get working together on the difficult task ahead - restoring American to the greatest airline in the world."
With the merger of American and US Airways completed in December, now the hard work begins to combine technology and reservation systems, which will not happen until 2015, and combining frequent-flier programs, labor contracts, and policies ranging from pets to baggage fees.