The trio suffered knocks in Ea Lla Koto's 5-2 loss to Mamelodi Sundowns in Orkney on Sunday.
According to Stars' website, new signing Nkausu is expected to be out for four weeks with a grade two muscle tear.
Fellow defender Shabalala's season is all but over after he tore a ligament, while striker Ngcobo fractured a facial bone in only his second start for the team since returning from a three-month lay-off.
Italian coach Giovanni Solinas is already without injured forwards Andrea Fileccia and Moeketsi Sekola, although the latter could feature next week after making a quicker than expected recovery.