South Africa took an early lead through an own goal by Kenya defender Amos Wanjala in the ninth minute, but the visitors fought back to level the contest before half-time.
Kenya captain Michael Olunga converted a penalty in the 44th minute to make it 1-1 and give the Harambee Stars renewed belief.
Mofokeng restores South Africa's advantage
South Africa continued to push forward after the break in search of another goal.
Their efforts were rewarded in the 77th minute when Relebohile Mofokeng found the net to restore Bafana Bafana's lead.
However, Kenya refused to surrender and produced a late response. Ryan Ogam struck in the 90th minute to secure a valuable equaliser for the visitors.
The late goal silenced the home supporters and ensured the two sides shared the points.
South Africa remain top of Group D
The draw means South Africa miss the opportunity to collect all three points, although they remain in a strong position in Group D.
Kenya, who have already qualified for the 2027 AFCON as co-hosts, will take confidence from their performance against one of Africa's established national teams.
The two countries will meet again on Tuesday, 17 November, when Kenya host the return fixture at Nyayo National Stadium in Nairobi.