Thole gets $1.25 million in each of the next two seasons. Happ receives $3.7 million this year and Bonifacio $2.6 million. The deals avoided salary arbitration.
Projected as the team's sixth starter, Happ was 10-11 with a 4.79 ERA in 24 starts and four relief appearances last season, striking out a career-high 144. The 30-year-old is 35-35 with a 4.19 ERA in six seasons with Philadelphia, Houston and Toronto.
The 27-year-old Bonifacio, acquired along with Jose Reyes in the November trade with Miami, hit .258 last season with one homer, 11 RBIs and 30 steals in 33 attempts.
Acquired from the Mets in the R.A. Dickey trade last month, the 26-year-old Thole hit .234 with one homer and 21 RBIs for New York last year.