The prestigious award was announced in the December issue of Swimming World, published on Wednesday.
Phelps was the first American man to win since Mike Barrowman in 1989 and 1990. Stockbauer was the first German to be recognised as the world's top female swimmer since Franziska van Almsick in 1993.
Phelps, 18, was the unanimous choice after winning three individual gold medals at the world championships in Barcelona.
During the course of the year he broke world records eight times in four different events -- the 100 and 200 meter butterfly, and the 200 and 400 meter individual medley.
He also set American records in the 200 and 400 meter freestyle and coach Bob Bowman has predicted Phelps will be even faster next year.
His prowess led to comparisons with the great Mark Spitz and speculation that in Athens next year the teenager will try to equal Spitz's astonishing feat of winning seven gold medals, all in world record time.
Japan's Kosuke Kitajima, who set world records in the 100 and 200 meter breaststroke to win gold in Barcelona, was second and Russia's Alex Popov, winner of two individual events at the World Championships, placed third.
Australia's Ian Thorpe, who has won the award for the past two years and four of the last five, was fourth.
Stockbauer, 21, was the only swimmer beside Phelps to win three individual gold medals in Barcelona and also set a European record in the 1500 meters freestyle.
Close behind her in the balloting was Ukraine's Yana Klochkova, a double winner at the world championships, followed by Amanda Beard of the United States.
Stockbauer, who swims for her hometown SSG Erlangen club, blossomed into the world's best female distance swimmer this year.
At the year's end, she remains the only woman to rank first globally in three events: the 400, 800 and 1500 meters freestyle.
