Johnson gets $6,375,000, a raise from $5.85 million. Villanueva receives $2,277,500, up from $1,415,000. Francisco's salary is $1,537,500, a raise from $1,175,000.
Johnson was acquired Aug. 23 from Arizona and hit .270 with three homers and nine RBIs for the Blue Jays.
Villanueva was 6-4 with a 4.04 ERA last year in 13 starts and 20 relief appearances. He is 26-28 with a 4.28 ERA in 40 starts and 223 relief appearances with Milwaukee and Toronto.
Francisco was acquired last month from Philadelphia after hitting .240 with six homers and 34 RBIs for the Phillies last year.
The Blue Jays also gave infielder Mark Teahen his unconditional release. Toronto acquired the 30-year-old Teahen from the Chicago White Sox on July 27. Teahen hit .200 last season in 78 games with Toronto and Chicago, with four home runs and 14 RBIs.