With regular captain Darren Fletcher missing and deputies Kenny Miller, Gary Caldwell and Scott Brown all absent from the squad, Morrison will skipper the side in Zagreb on his 27th international appearance.
Meanwhile, a bout of tonsillitis has denied defender Gordon Greer a possible Scotland debut.
The Brighton defender was called up for the first time by manager Gordon Strachan but has not been able to travel.
His withdrawal leaves Scotland with only two recognised centre-halves; Grant Hanley and Andy Webster.
However, Russell Martin could provide Strachan with an option in central defence.