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 5, 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.
