Phelps's financial support has also been cut off for the same three-month period, the sport's national governing body said in a statement on its website on Thursday.
"This is not a situation where any anti-doping rule was violated, but we decided to send a strong message to Michael because he disappointed so many people, particularly the hundreds of thousands of USA Swimming member kids who look up to him as a role model and a hero," the federation added.
"Michael has voluntarily accepted this reprimand and has committed to earn back our trust," the statement said.
The photograph, said to have been taken at a November party at the University of South Carolina, was published by British tabloid newspaper News of the World last Sunday.
Phelps accepted the ban, saying he understood USA Swimming's "point of view," the swimmer's spokesman Drew Johnson said.
"He feels bad he let anyone down," Johnson added. "He's also encouraged by the thousands of comments he's received from his fans and the support from his many sponsors. He intends to work hard to regain everyone's trust."
Phelps has repeatedly apologised for the incident and said he may backtrack on his plans to compete at the London Olympics in 2012.
The International Olympic Committee said his apology was proof of his sincerity and the world swimming's governing body FINA is also backing the embattled swimmer.
Phelps has won 14 career Olympic gold medals, making him the most successful competitor since the modern Olympics began 113 years ago.