Sifiso Vilakazi and Brett Evans scored the Urban Warriors, while Ruben Cloete netted for Ea Lla Koto.
It took the home side just eight minutes to register their first goal, which was created by the brilliance of Sameehg Doutie, who showed sublime skill to beat his man and whip in a tantalising cross for Vilakazi, who buried the ball with a powerful header.
Saitjheni Tsotetsi should have equalised for Ea Lla Koto three minutes later when he was played through on goal by an intelligent ball by Thamane Motaung, but a poor finish saw the ball fly high over the bar.
While Stars had the occasional burst forward, it was Ajax who looked more purposeful and creative in their play and they were rewarded in the 22nd minute when Brett Evans' deceptive free kick crept into the far post.
The remainder of the half saw the Urban Warriors looking the more offensive of the two sides and they created several more chances, although these were confined to long range efforts from the likes of Franklyn Cale and Dipsy Selolwane, none of which troubled Stars keeper Kennedy Mweene.
The Free State side started the second half in a positive vein and dictated matter early on.
They played several crosses and free kicks into the Ajax box and in came close to scoring after 47 minutes when Duncan Lechesa's header flew just over the cross bar.
Ajax goal keeper Andre Petim ensured his side maintained their two goal cushion when he pulled off a good save to stop Motaung from scoring from the edge of the area in the 67th minute.
At the opposite end of the field Mweene was also given work to do when he was faced with a Cale free kick - the Stars goal minder was lucky not to concede a third when he allowed the ball to squirm through his hands.
But Stars had put in a good effort in the second stanza and their toil was rewarded with a goal five minutes from time when Ruben Cloete buried a powerful free kick into the bottom corner of the goal.
It was however too little too late as Ajax had no problem defending their lead for the final minutes of the game.