Relebohile Mofokeng put the hosts 2-1 ahead after Kenya defender Amos Wanjala had scored an early own goal, but Bafana failed to hold on as Benni McCarthy's Harambee Stars snatched a late equaliser.
Despite controlling possession for much of the contest, South Africa struggled to capitalise on their scoring opportunities, something that left Mosimane particularly frustrated. The former Mamelodi Sundowns coach acknowledged that his players' wastefulness had cost them victory.
"That's football for you; two goals were not enough. Playing good football is not enough; pretty football is not all about that," Mosimane told the media.
"You need to take the chances, and ball possession doesn't win games. So that's the reality, that's what you see, that's the lessons we get from here."
The result marked Bafana's first dropped points in Group D, having previously beaten Guinea 2-1 and Eritrea 5-0. Mosimane had also overseen a friendly victory against Egypt since returning to the national team.
South Africa now hold just a one-point cushion over second-placed Guinea, missing the chance to extend their advantage to three points. Nevertheless, Mosimane maintained that his team remained in control of the group.
"But I think we want to qualify the hard way. I think we want it the hard way. But for me, it's to stay where we are on the log and finish where we are on the log," Mosimane added.
"So, it's still in our hands, but it's sad. It's bitter, but it's part of the game. Now we can see the character we have in the team.
"Can we fight? Can we stay where we are? Because we have worked hard to be where we are and with the centre-backs you might not like. But we are where we are."
Bafana Bafana head coach Pitso Mosimane found himself at the centre of attention after reacting angrily to questions about his decision to leave Mbekezeli Mbokazi out of the starting line-up against Kenya.
Ghana revived their hopes of reaching the 2027 Africa Cup of Nations with a 2-0 victory over Somalia in this week's Group C encounter at the Sekondi Sports Stadium.
Relebohile Mofokeng stood out for Bafana Bafana in their 2-2 draw with Kenya in the 2027 AFCON qualifiers on Friday, while the defenders had a tough outing.
Bafana Bafana dropped their first points in the Africa Cup of Nations qualifiers when they were held to a 2-2 draw by Kenya at the Orlando Amstel Arena on Friday.
