Ntseki had to made six changes to his squad because of the withdrawal of players due to injuries and medical issues.
Speaking after their last training session on Thursday evening, the coach said although it has been challenging to make unplanned changes, focusing on the aim of getting a win is something they can still control.
"We had players who had to play their last matches before reporting for camp, so it's been a challenge because we saw the withdrawal of Reeve Frosler, Bradley Grobler and Thulani Serero due to injuries and the rest of the guys it was conditions of medical reasons," he said.
"But we are looking forward to the game, we can't be worried about things we can't control, we are more concerned about things we can control, going to the match, doing well and winning."
Most of the players in the national team camp are on form and Ntseki admitted that coming up with the final starting line-up to face Sao Tome at Moses Mabhida Stadium will be a good headache.
All the players are available for selection besides Thabo Nodada, who did not finish the morning session on Wednesday. Overseas-based Bongani Zungu and Kamohelo Mokotjo might start on the bench due to only having a few sessions due to lengthy travelling.
"Our last player [to arrive] Bongani Zungu had to travel for 22 hours, which was bit too much for him. Kamohelo Mokotjo also had to travel 24 hours coming from America," Ntseki explained.
"But the good thing us they are all here and we've been preparing with conditions that we expect to be faced with come the kick-off time.
"Everybody has 100 percent chance to be selected and play for his country, but in football we know we have to come with the first eleven and we can always keep the strongest eleven on the bench to make sure whenever we need any of them they can come in and add value to the team and change the face of the game."
Ntseki is confident that he has selected top players who will deliver maximum points over the two legs, which would give South Africa a huge opportunity to guarantee their spot at AFCON 2021.
"That makes us feel happy and confident as we are going to this match knowing that it's not much of a headache [to lose players] but all that is important is that we've brought the best in the country," he added.
"Yes of course we've had some withdrawals, but the current team that we have is the strongest we can think of currently."