The win has moved the Free State outfit up to seventh spot, while the Urban Warriors find themselves in 14th place.
Ea Lla Koto were the more threatening side in the opening exchanges albeit without creating any clear opportunities.
Ajax couldn't convert a double chance midway through the first half as Tashreeq Morris and Grant Margeman missed after being set up by Ejike Uzoenyi.
Edward Manqele then drew first blood for Stars in the 43rd minute as the hosts headed into halftime with the advantage, 1-0.
Stars doubled their lead just five minutes into the second half through a Mohammed Anas strike, 2-0.
Morris unleashed a fierce shot which struck the underside of the post in the 66th minute as Ajax looked to get back in the game.
However, in the end Luc Eymael's charges walked away with three points as Ajax once again faltered in the Free State.