South Africa need to overturn the east African side over two legs to qualify for the CHAN tournament taking place in Kenya, Tanzania and Uganda from 2–30 August 2025.
Bafana looked to be on course for at least a draw at the Bingu National Stadium in Lilongwe on Saturday, until an 89th minute winner.
Ntseki praised Malawi for their performance, while admitting to being disappointed that Bafana lost the first leg.
He said on iDiski Times: "Congratulations to Malawi. They were playing at home. Very much under pressure to win.
"When you look at the supporters that came to support the team, they were expecting something from the team.
"We think we did very well in terms of keeping them at bay until that late critical phase mistake of allowing a corner and then we failed to defend the corner.
"But, on the balance of play, I think it was a very interesting match. It was more of a two and flow type of a game. But you can tell these are the players that are playing regularly. These are the players that some of them are playing in the national team."
Ntseki added: "So, from our side I think we did very well when you look at none of the players we had today are playing regularly in their teams.
"So, you can tell those critical phases of the game, the concentration levels dropped a bit and as a result, we ended up giving the goal.
"But I think credit must be given to the players with the effort they had to put in this game as difficult as it was. We have to go back home and and then look into how best we can reverse the results at home.
"Hopefully, things works out for us but we are disappointed to have lost the game."
The two sides clash again at Loftus Stadium on Sunday 11 May 2025.