Godfrey, who will leaving effect Dec. 31 after an eight-year run, said he decided not to seek a new contract with the American League franchise.
"I indicated this possibility to the ownership of the Toronto Blue Jays baseball club earlier this year," he said.
"I would like to thank (owner) Ted Rogers for the opportunity to fulfill every sports fan's dream of running a major league franchise."
Toronto finished fourth in the AL East this season with an 86-76 record, 11 games behind the division-champion Tampa Bay Rays.
Martin Bashir resigns from MSNBC over Sarah Palin comments
Ron Burgundy interviews Peyton Manning on SportsCenter