Ea Lla Koto advanced courtesy of second-half goals from Danny Venter and Abdul Basit Adam at Goble Park Stadium.
Stars joined Golden Arrows - who parted ways with coach Manqoba Mngqithi today - and SuperSport United in the next round of the competition.
The home side came close to opening the scoring in the third minute when Camaldine Abraw nudged the ball past the approaching Tapuwa Kapini, but Tamsanqa Teyise covered his captain with a good clearance before the goal line.
Abraw continued to cause problems for the visitors and in the ninth minute he found Venter unmarked in the centre of the box, but the winger slipped before his goalbound shot was deflected wide of goal.
Then moments later Adam had another opportunity to hand his side the lead when he met a low cross at the near post, but the Ghanaian striker volleyed over the bar from a few yards out.
The visitors started to push forward more during the second part of the first stanza, but Marc van Heerden saw his teasing cross headed away in the 21st minute, before firing over the crossbar nine minutes later.
Steve Komphela's outfit almost broke the deadlock on the stroke of half-time when Abraw was given space to shoot outside the box, but Kapini made a good block to keep the volleyed effort out.
Ea Lla Koto were handed a chance to take the lead four minutes after the break when Larry Horaeb slipped just outside the box; Reuben Thebakang raced into the area but his shot was blocked by Carlington Nyadombo.
Kapini then pulled off two superb saves to deny Katlego Mashego in the 52nd minute.
The opening goal arrived in the 63rd minute when Venter controlled the ball on the edge of the area and took one step in before firing a left-footed shot past Kapini.
The visitors had numerous opportunities to equalise, but Teyise sent his header wide in the 69th minute, while Goodman Dlamini saw his shot dipping inches match in the over the crossbar four minutes later.
In the 79th minute, Ayanda Dlamini ran onto Van Heerden’s cross, but the ball came off his chest and dipped over the crossbar before Bongani Ndulula headerdwide of the upright a minute later.
Stars goalkeeper Daniel Agyei made his first real save of the match in the 83rd minute, diving low to his right to block a solid strike from substitute Sthembiso Ngcobo.
The hosts then doubled their lead three minutes later through a well-taken goal from Adam, who beat Kapini with a dipping volley from outside the box.
Usuthu had two more opportunities to pull one goal back, but G. Dlamini fired wide in the first minute of added time, while Ngcobo was denied by a brilliant tackle from Soriola Gege three minutes later as Stars held on for a 2-0 win.