Eagles set the tone in the opening five minutes after Thapelo Selepe played in Modibedi Mokoena for an opportunity at goal.
Motlatsi Perekisi missed a clear opportunity after failing to get a proper shot on goal after 12 minutes, while Ea Lla Koto got their first effort on goal two minutes later through Nhlanhla Vilakazi.
Another opportunity went a bagging after Siphelele Mthembu made hard work of a ball inside the box by failing to get his header in control.
The former Orlando Pirates and Kaizer Chiefs man then failed to put his side in front with the half’s best chance after missing from the penalty spot following an altercation in the box five minutes to the break.
Veteran striker Nkosinathi Ogle failed to make them pay three minutes later after breaking through the defence only to balloon over the top.
The NFD side eventually made them pay after Bongani Mbuli stepped up to give them a one goal lead on the stroke of half time.
The visitors pulled out the big guns at the start of the second half following the introduction of Maxime Cosse for Sthembiso Dlamini.
Vilakazi got goal-side once more after 61 minutes but failed to draw the host level with the game running away from them.
Phukalla Ntsu were looking to increase their tally thanks to Ricardo Versuur after the launch of a quick counterattack but it went astray later on.
Luc Eymael’s side found the equaliser on the stroke of full time through Rooi Mahamutsa to send the game into 30 minutes of extra time.
They took the lead for the first time in the game after Ghanaian Mohamed Anas stepped up inside the box to riffle home from close range for a last 16 spot.
Eagles: Ramalele, Hlela, T. Mokoena, Perekisi (Nkosi 100’), Versuur, Mbuli, Maduna, M. Mokoena, Selepe, Ngwenya (Setsumi 66’), Moloi.
Subs: Esterhuizen, Ogle, Setsumi, Nkosi, Lepele, Likontsane, Fabien.
Stars: Ngobeni, Phungwayo (Mokhuone 86’), Mahamutsa, Keita, Mashego, Masehe, Vilakazi, Jantjie (Anas 68’), Dlamini (Cosse 57’), Tchilimbou, Mthembu.
Subs: Mobbie, Anas, Makhehlene, Relebogile, Mbhele, Sangare, Cosse.