Norwich City midfielder Clingan aggravated a shoulder knock in the weekend defeat to Derby County, while Motherwell defender Craigan is struggling with a pelvic injury.
Both players featured for their clubs at the weekend, but will not be included in Worthington's plans for Northern Ireland's Group Three clash in Maribor.
Speaking last night, Worthington said the duo's absence would be sorely felt as he looks to boost his World Cup fortunes with three points.
"Sammy was involved in a crunching tackle during Saturday's game and hurt his shoulder, so I am satisfied that the injury is bad enough to rule him out," the international boss said.
"He was desperate to play on Saturday, and he is gutted at missing out on another Northern Ireland cap. It is disappointing but we have to cope without Sammy in Slovenia.
"Stephen is another big blow because he has played so well for his country in the heart of defence. If there is a plus point, it would be that we have some strength in depth at the back."
Worthington admitted Clingan could feature in the home fixture with San Marino at Windsor Park next week if he recovers from his shoulder injury.
"I will be monitoring Sammy's progress over the next few days and keeping in touch with him," the Northern Ireland boss added.
"Hopefully Sammy can get some good rehabilitation under his belt and be drafted in for the game with San Marino. I obviously want my strongest squad for both games so I will be holding out for Sammy for next week's game."
Meanwhile Burnley defender Michael Duff has also been withdrawn after sustaining a hamstring injury.
Duff joins, Craigan, Clingan and West Bromwich Albion's Chris Brunt, who pulled out last week because of a back injury.
Scunthorpe midfielder Grant McCann and Manchester City's rookie defender Ryan McGivern are the only players drafted in so far.