Bafana will not be among Africa's 24 best teams in Cameroon next year when the continental showpiece will be staged, after they lost 2-0 to Sudan on Sunday evening.
Ntseki's charges played to a 1-1 draw with Ghana at FNB Stadium last Thursday and needed only a point to seal their spot at the AFCON finals but completely bottled the job.
Having failed at the mandate, the 51-year-old former under-17 national team head coach has accepted responsibility and expressed grave disappointment at letting South Africa down.
"I think as a head coach of Bafana Bafana, I came up with a turn-around strategy and I think everything started very well, because we managed to accumulate 10 points and needed only a point to qualify," Ntseki told SAFA media after the match.
"Yes, as a coach, as head of the selection committee, as head of the team, my disappointment is huge – it's huge for my personal growth and my personal achievement as coach of Bafana Bafana.
"The success of the team is my success, and the failure of the team firstly starts with me – to say, 'I have failed as a coach', because in football we need to own up.
"When there is success, you become everybody's favourite but when there is failure, you become and orphan and everybody looks at you and says, 'You failed the team; you could not qualify.'
"But things like this do happen in football, and we own up... It's a big disappointment for myself."