The team will also wear a No. 32 patch on their uniforms this season in honor of Halladay, who died last year in a plane crash.
Hall of Famer Roberto Alomar's No. 12 is the only other uniform number of a former Blue Jays player retired by the franchise.
"Through Roy's values, pride, work ethic, and perseverance, he epitomized what it means to be a Blue Jay," team president Mark Shapiro said in a statement. "And while his legacy is clear, it goes far beyond the number on his back or his on-field accomplishments, serving as a shining example of how to live a meaningful life and positively impact others."
Halladay pitched 12 seasons for the Blue Jays, winning the AL Cy Young in 2003, when he went 22-7 with a 3.25 ERA. He is second all time in wins in franchise history with 148.
Halladay, an eight-time All-Star who also won a Cy Young with the Philadelphia Phillies in 2010, died on Nov. 8 when his plane crashed into the Gulf of Mexico. He was 40 years old. An autopsy report said the pitcher had evidence of amphetamine, morphine and an insomnia drug in his system.