FINA president Julio Maglione presented Phelps with a silver trophy to recognize his achievements.
Phelps pushed the United States in front to win the medley relay Saturday in the final swimming event of the London Games, after which he is retiring.
He leaves the sport with a record 18 golds and 22 medals overall.
At the 2008 Beijing Games, Phelps won eight golds, one more than the previous record of seven at one games held by fellow swimmer Mark Spitz.
At these games Phelps won four golds and two silvers — again more medals than any other swimmer.