Ricciardi, the director of player personnel for the Oakland Athletics the last three seasons, was hired as senior vice president/baseball operations and GM. He replaces Gord Ash, who resigned in early October.
The selection of the 42-year-old Ricciardi capped an exhaustive search by Blue Jays CEO Paul Godfrey, who was believed to be interested in Buck Showalter, the former manager of the Arizona Diamondbacks, as well as former Texas Rangers GM Doug Melvin.
Godfrey also held interviews with John Hart, who opted for a $2 million-a-year contract to be the GM of the Rangers, and Florida president and GM Dave Dombrowski, who last week was named president of the Detroit Tigers.
Philadelphia Phillies Assistant GM Mike Arbuckle and Jays assistant GMs Stewart and Tim McCleary also were mentioned as candidates.
The Toronto Sun reported Wednesday that Stewart stepped down in protest, claiming that baseball was a "shallow industry" that was not committed to minority hiring in the front office.
"I don't want to do it anymore," Stewart told the Toronto Sun.
"I'm losing faith and losing hope."
A Blue Jays spokesman would not confirm that Stewart, who is black, has left the organization.
Ricciardi was a key assistant for Oakland GM Billy Beane and he helped build a team that features young pitchers Tim Hudson, Barry Zito and Mark Mulder. Oakland won 102 games last season, the second-highest total in baseball.
A veteran of 21 years in baseball as a player, coach and scout, Ricciardi had been with Oakland the past 15 years.
Riccardi was an infielder in the New York Mets organization, and went on to work for the New York Yankees before joining the Milwaukee Brewers as a minor league coach and manager.
Ricciardi is expected to have a budget of about $75 million to improve a team that was just 80-82 last season under first-year manager Buck Martinez.
Ash, a Toronto native, has been with the organization since 1978 and has been general manager since 1994. He took over for Pat Gillick, the architect of World Series championship teams in 1992 and 1993.
Under Ash, the Blue Jays went from the best team in baseball to an also-ran in the American League. They had losing seasons from 1994-97 and never won more than 88 games, playing in front of sparse crowds at once popular SkyDome.