Gibbons, 50, followed John Farrell, who left the Blue Jays after two seasons as manager to take a similar position with the Boston Red Sox. Toronto was 154-170 under Farrell.
Gibbons managed the Blue Jays for parts of five seasons, fashioning a 305-305 record. He was fired 74 games into the 2008 season. His best season was 2006 when the team went 87-75 and finished second in the AL East. The 610-game tenure was the longest for a Toronto manager since Cito Gaston's 1992-97 tour.
The Blue Jays on Monday completed a trade with Miami that gives Toronto pitchers Josh Johnson and Mark Buehrle, shortstop Jose Reyes, catcher John Buck and outfielder Emilio Bonifacio. The Blue Jays also agreed to a deal with free-agent outfielder Melky Cabrera.