Toronto announced the hire on Thursday. Montoyo will officially be presented as the franchise's 13th manager at a news conference on Monday at Rogers Centre.
"I am extremely honored and humbled to join the Toronto Blue Jays organization, and I would like to thank Mark [Shapiro] and Ross [Atkins] for this amazing opportunity," Montoyo said in a statement.
"Managing a team that represents an entire nation is incredibly special. My family and I look forward to working towards the ultimate goal of winning a championship for this city. I also want to recognize the entire Tampa Bay Rays organization for giving me the chance to start my coaching career."
The Jays announced on Sept. 26 that John Gibbons would not return as the team's manager in 2019. Gibbons, 56, joined the Jays in 2013. He posted a 791-787 record in 1,578 games as the team's manager. The Jays finished in fourth place in the American League East this season with a 73-89 record.
Montoyo signed a three-year contract with a club option for 2022. He also interviewed with the Cincinnati Reds. He spent 18 years as a manager in the Rays' Minor League system.