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Pitso Mosimane's charges were on course for a third consecutive victory in Group D, but Ryan Ogam netted for Kenya on the stroke of full-time to salvage a point for the visitors.
Bafana remain on top of the group on seven points, one point ahead of Guinea, while Kenya - who will co-host AFCON next year - claimed their second point of he campaign and sit in third place.
It was the Harambee Stars that almost opened the scoring in the first few minutes when Adam Wilson saw his volley topped over the cross-bar by home goalkeeper Ronwen Williams.
Bafana gradually got into the contest and created a few chances as Iqraam Rayners and Tshepang Moremi went close to opening the scoring.
Kenya were then their own worst enemies as they conceded a calamitous own goal when Amos Wanjala played a horrendous back-pass then ended up his own net to giver the home side the lead.
Former Bafana striker Benni McCarthy, now in charge of Kenya, watched on as his team fought back when Bafana conceded a penalty as Thabang Matuludi was adjudged to have handled the ball in the box.
Michael Olunga stepped up and converted the spot-kick as to give the Harambee Stars parit on the scoreboard as the teams went into the half-time break.
Bafana came out with good attacking intent after the interval and visiting goalkeeper Bryne Omondi made a brilliant save to deny Rayners and keep the score level.
The hosts were not disheartened though and took the lead again with 20 minutes remaining when substitute Lyle Foster and Relebohile Mofokeng combined before the latter volleyed home.
McCarthy's charges showed all the fighting qualities that he had as a player and Ogam had the final say as he danced through a couple tackles before beating Williams to make the score 2-2.
The teams will clash again on Tuesday when they meet at the Nyayo National Stadium in Nairobi.