The other women's nominees were world champion shot-putter Valerie Adams of New Zealand, and world hurdles champion Zuzana Hejnova of the Czech Republic.
"I'm shocked and excited. It's something that has been a dream of mine," said Fraser-Pryce, who is the second Jamaican woman to win after Merlene Ottey in 1990. "Hard work is something that comes without saying for us to achieve the things we want."
Both winners also received $100,000.
Jamaica's anti-doping program was audited by the World Anti-Doping Agency after a former Jamaica director alleged it didn't drug-test its athletes for entire months before they dazzled at the London Games.
The ex-director, Renee Anne Shirley, indicated a near-complete breakdown in the agency's out-of-competition testing from January 2012 to the Olympics.
Before the Herculis meeting in July, Fraser-Pryce walked out of news conference in Monaco after doping questions following positive doping tests by American sprinter Tyson Gay and Jamaica's Asafa Powell.
Powell, the former 100 world record-holder, and compatriot Sherone Simpson, a three-time Olympic medalist, tested positive for a banned stimulant at the Jamaican championships. Three-time Olympic gold medalist Veronica Campbell-Brown of Jamaica tested positive for a banned diuretic in May.