It was the final individual race of the 27-year-old's career, which will end tomorrow night in the 4 x 100m Medley Relay.
Tonight, the Baltimore swimmer was seventh at halfway, with Milorad Cavic first, before the USA swimmer produced a customary storming final length to touch in 51.21.
Phelps finished ahead of Chad le Clos, his conqueror in the 200m, and Evgeny Korotyshkin, who shared second place.
Earlier, teenager Missy Franklin claimed gold in the women's 200m Backstroke in a new world record time.
Franklin lowered Kirsty Coventry's world mark set in 2009 by 0.75 to 2:04.06.
Anastasia Zueva of Russia finished second, with USA's Elizabeth Beisel third.