Jefferies was sent to the stand during Kilmarnock's 2-0 defeat at Celtic in the SPL on January 2, after being accused of adopting a "threatening manner" towards linesman Brian McGarry by referee Steve Conroy.
The Killie boss claimed he simply laughed when McGarry failed to award his side a foul, and launched an immediate appeal against the suspension which followed.
Jefferies made his case to the SFA on Tuesday morning and told reporters he had been cleared as he left the Hampden meeting.