Boozer also grabbed eight rebounds as Chicago held on for a fourth straight win.
After the Bulls turned the ball over on shot clock violation with 10 seconds left, Butler swatted aside DeMar DeRozan's potential go-ahead jumper with 2.4 seconds remaining.
He later added a free throw to seal the victory, finishing with 16 points, six assists and six rebounds.
The Raptors had their three-game winning streak snapped despite 32 points from DeRozan.
Kyle Lowry supplied 16 points, seven assists and five rebounds.