SuperSport took control from the onset with Reneilwe Letsholonyane and Teboho Mokoena controlling the game from the middle of the park.
For all of their possession, chances were hard to come by as Ke Yona goalkeeper Mduduzi Khumalo enjoyed a quiet opening 30 minutes.
Eric Tinkler's charges eventually broke the deadlock after 37 minutes when Phala found the back of the net with a low drive from 18-yards out.
SuperSport's lead was doubled on the stroke of halftime as Modiba headed home Siyabonga Nhlapho's cross from the right flank.
Tinkler opted for a triple change at the start of the second half, as new signing Azubuike Egwuekwe, Letsholonyane and Kingston Nkhatha made way for Grant Kekana, Sipho Mbhule and Prince Dube.
The Ke Yona team went close to reducing the deficit in the 65th minute when Zimele Zuma struck the crossbar from close range with Mondli Mpoto well beaten.
SuperSport enjoyed most of the possession in the second half and showed off some good combination involving Mokoena and Mbhule in the middle of the park.
The Ke Yona were rewarded for their perseverance in the final minutes of stoppage time when Zamuxolo Mduli fired into an empty net following an error from Mpoto.
Nevertheless, 2-1 is how the encounter finished as SuperSport won the trophy for a second successive year while the Ke Yona team scored their first ever goal since the inception of the Ke Yona Challenge.
SuperSport will now shift their focus to next weekend's second leg MTN8 semi-final clash with Maritzburg United.
Ke Yona: Khumalo, Xulu, Hlongwane, Mgotlane, Mpholo, Nhamuchua, Sam, Manyama, Ximba, Plaatjie.
SuperSport: Mpoto, Nhlapo, Mashamaite, Egwuekwe, Boateng, Mokoena, Letsholonyane, Modiba, Myeni, Phala, Nkhatha.