The goals were scored by Bevan Fransman and Sandile Ndlovu.
Swallows were off to a bright start when James Mayinga had a go from long range that came close and Mark Haskins had his shot from inside the box saved by Kalililo Kakonje.
AmaZulu striker Mpho Maleka missed a good chance to put the hosts ahead after 21 minutes when he fired over the bar from close range.
Thapelo Mosetlhe did likewise for Swallows when he shot wide from 12-yards out after 24 minutes.
It was Usuthu however who carved out more opportunities in the opening half, with Masoeng Sillo having two goal attempts, followed by shots from Belux Bukasa Kasonga and Thulani Mhlongo.
But having missed several chances, AmaZulu paid the price in the 44th minute when Birds defender Bevan Fransman struck from close range, beating the offside trap after a pass from Japhet Zwane.
Swallows were immediately onto the offensive in the second half, with Japhet Zwane firing a shot over the bar from the edge of the area in the 46th minute, while Sandile Ndlovu's powerful shot went wide of target 10 minutes later.
Haskins had another chance to get his name on the score-sheet, but missed the target from the left hand side of the box in the 63rd minute.
The Birds' dominance was finally rewarded in the 76th minute when they received a penalty after Siboniso Gumede brought down Tshweu Mokoro inside the box.
Ndlovu made it 2-0 when he stroked home the penalty kick.
To their credit, AmaZulu refused to give in and pushed forward in search of a goal. But the likes of Bulelani Matross, Maleka, Thabo Mabaso and Mohammed-Awal Issah were all unable to find a way past Birds keeper Greg Etafia late in the game.