McIntyre was sacked by Dunfermline who sit bottom of the SPL last week after just over four years in charge of the fife side.
Jefferies, who has been without a club after being shown the door at Tynecastle in August, has the task of saving the club from relegation.
Chairman John Yorkston commented: “We are delighted to secure the services of someone with a proven track record, someone with such a vast experience in football management.”
Jefferies first game in charge could be Dunfermline’s home game against St.Mirren on Saturday.
