Molina will receive a $1.5 million signing bonus and a $3 million salary this year under the agreement, and the deal contains a $7.5 million mutual option for 2007 with a $500,000 buyout.
Molina spent his first eight years with the Los Angeles Angels and hit a career-best .295 last season with 15 home runs and 69 RBI. He won Gold Glove Awards in 2002 and 2003.
The New York Mets spoke with Molina in November and offered an $18 million, three-year contract. New York then had the chance to acquire Paul Lo Duca from the Florida Marlins and withdrew the offer to Molina before negotiations really began.
Toronto expects to be a contender in the AL East after having an extremely active offseason. Among the players with major-league experience who the Blue Jays added: right-hander A.J. Burnett, closer B.J. Ryan, third baseman Troy Glaus, first baseman Lyle Overbay, infielder John McDonald, catcher Jason Phillips, left-hander Brian Tallet and right-hander Ben Weber.
Phillips and Weber were signed to minor-league contracts.