Ricciardi, the director of player personnel for the Oakland Athletics the last three seasons, was hired as senior vice president/baseball operations and general manager.
He replaced Gord Ash, who resigned in early October.
The selection of the 42-year-old Ricciardi capped a 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 contract to replace Melvin in Texas. Florida president and GM Dave Dombrowski, who last week was named president of the Detroit Tigers, also was in the running.
Stewart was mentioned as a possible candidate but reportedly 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."
The Blue Jays would not confirm that Stewart has left the organization, but the Milwaukee Brewers announced Wednesday that Stewart had agreed to be their pitching coach in 2002.
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 and a talented infield. 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.
"I am very excited for J.P. and his family for this tremendous and well-deserved opportunity," Beane said. "J.P. is recognized as one of the best talent evaluators in the game and his contributions to the A's are evident throughout our entire organization.
"He will be difficult to replace. While he will be missed professionally, I will miss him more on a personal level because he has been like a brother to me. I consider him my closest friend in the game."
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 in the hopes of improving a team that was 80-82 last season under first-year manager Buck Martinez.
Ash, a Toronto native, had been with the organization since 1978 and served as the general manager since 1994. He took over for Pat Gillick, the architect of World Series championship teams in 1992 and 1993.