The former Olympic champion and 200m freestyle world record holder is Italy's most high-profile female sports star.
"This is the crowning moment of years and years of a career comprising great defeats and really great victories," she said in a Tweet after the announcement.
Coni said her selection had been "written in the stars" as the opening ceremony in Rio's legendary Maracana stadium is on August 5th, Pellegrini's 28th birthday.
"It will crown a dream career that has always been pursued under the signs of talent, sacrifice and passion," the Olympic committee said.
The glamorous Pellegrini won the 200m freestyle gold in Beijing in 2008 but failed to secure a single medal at London 2012.
She is a four-time world champion having won both the 200m and 400m in 2009 and 2011.
Pellegrini made headlines recently when she inadvertently posted her mobile phone number on Twitter, on which she has nearly half a million followers.
The mistake resulted in an avalanche of requests from admirers for her WhatsApp details as well.