The Durban club are now 12 points ahead of second-bottom Jomo Cosmos with three games left to play.
A lone goal from Ghanaian Mohammed-Awal Issah seconds after halftime was enough to seal the points for Usuthu, and hand them the perfect confidence boost ahead of their Nedbank Cup semifinal against Mamelodi Sundowns on Sunday.
Wits now face an uphill battle to earn a place in the top eight, having slipped to 10th after at one time being touted as possible championship contenders.
The home side did have the lion’s share of the possession and chances, but failed to unduly trouble Kalilio Kakonje in the visiting goal.
And they were made to pay for their wastefulness in front of goal when Issah converted Mpho Maleka’s cross almost from the kick-off for the second period.