Beeston, the club's president and CEO through their World Series glory days, was the club's CEO from 1976 through 1997.
It will be Beeston's job to find a successor to Godfrey.
It marks the second time this season that the Jays have gone back to the future. On June 20, they brought Cito Gaston back as their manager after firing John Gibbons.
"Make no mistake, I'm not here to work full time," Beeston said. "I don't expect to be there for spring training."
The signing of Beeston has fueled rumors that he will be talking with Pat Gillick, the former Jays general manager and the current GM of the Phillies, about taking on the job. Gillick has announced he would not be back with the Phillies in 2009.
Gillick, meanwhile, has shot down those rumors.