Happ and Bonifacio signed one-year deals worth US$3.7-million and $2.6 million respectively.
Thole signed a two-year contract worth $2.5 million, with a club option for the 2015 season worth $1.75 million.
Happ, projected as the team's sixth starter, was 10-11 with a 4.79 earned-run average in 28 games last season, including 24 starts between Houston and Toronto. The six-foot-six, 195 pound lefty won 10 or more games for the second time in his career, while posting a career high 144 strikeouts.
The 30-year-old has a 35-35 career record with a 4.19 ERA in six seasons with Philadelphia, Houston and Toronto. The Blue Jays acquired of his as part of a 10-player trade last season.
He batted .258 last season in 64 games, with 30 stolen bases in 33 attempts.
The five-foot-11, 200-pound switch hitter has played all three outfield positions as well as second base, third base and shortstop during his six year career with Arizona, Washington and the Marlins.
In 476 career games the Santo Domingo, Dominican Republic native has posted a .267 average with a .329 on-base percentage along with 53 doubles, 25 triples, seven home runs and 110 stolen bases.
Thole came to Toronto with National League Cy Young winner R.A. Dickey in an off-season trade with the New York Mets.
Thole will mostly be counted on to catch Dickey's knuckleball.
He hit .234 in 104 games last season for the Mets with 15 doubles, one home run and 21 RBIs.