The striker netted after 16 minutes with a clever header against his former side in a match the Students largely dominated, winning for the first time in 2014.
They looked the more assured side throughout and, during the opening half, could have gone ahead in the 10th minute when Calvin Kadi was played in on the right, but saw his effort blocked by the feet of Philani Zikalala.
After a wayward effort from Kulegani Madondo, the Students went in front courtesy of Ngcobo, who did well to drift back from his marker and loop in a fine header from a Faty Papy beyond the AmaZulu keeper.
Usuthu continued their battle to find openings and a frustrated Thamsanqa Teyise blasted over wildly from 40 yards, before Sifiso Hlanti wastefully thumped a free-kick over.
Gavin Hunt’s men had a golden chance to go two up after 36 minutes when debutant Jabulani Shongwe swung over a fine cross from the left which was ballooned over by Sibusiso Vilakazi from three-yards out.
Hlanti had another set-piece chance before the interval, and even though it was a much better effort, the ball still curled over.
After the break, January signing Shongwe failed to hit the target at the far post after a flick on by Ngcobo, while Siboniso Gumede did the same with a weaker effort through a crowd of players after a corner fell to his feet in the centre of the penalty area.
More dilly-dallying by the home defence almost allowed in Vilakazi on the hour mark, only for Zikalala to charge off his line and punch away the loose ball.
AmaZulu tried desperately to get back into the game, but struggled to carve out too many openings against one of the best defences in the league.
In the end the early goal settle the contest with Craig Rosslee’s men falling to fifth on the table.