Khumalo's Greek outfit PAOK defeated Bnei Yehuda 4-1 to take their third round qualifying tie 6-1 on aggregate.
Dino Ndlovu featured in what is likely to be his last outing for the Israeli team before he makes the move to Maccabi Haifa ahead of the new season.
It is a fine start to his loan spell at PAOK for Khumalo, whose major aim in the next nine months is regular first team football after playing just five first-team games in the whole of the 2011/12 season while at Reading and Tottenham Hotspur in England.
Ngcongca's Belgian club Genk had to overcome blistering heat as they defeated Kazakhstan's Aktobe 2-1 for a 4-2 aggregate success.
The Bafana Bafana right-back once again played in the role of centre-back, having been switched from his usual fullback position for this season.
Also through are Portuguese side Maritimo, who were held 0-0 at home by Greek outfit Asteras, but advanced on the away goals rule having managed a 1-1 draw in the first leg.
They have South African-born Sergio Marakis in their squad for the Europa League this season.
The draw for the next round of the competition will be made later on Friday, when the remaining South Africans will be made later on Friday in Switzerland.
Meanwhile, the draw will also be made for the playoff round of the Uefa Champions League, where May Mahlangu will find out who his Swedish side Helsingborg will play in the next round.