South African will welcome the Super Eagles on Saturday, November 17 in their fourth Group E match.
"Being confident means, the players that I have worked with I know they desire greatly to qualify," said Baxter to the media.
"They know that Nigeria are a top class team and will be on the other side of the field. They know we've got to get rid of that (win Nigeria) to get where we want to go,” he added.
The English mentor has an injury-ravaged squad as he misses the likes of Bongani Zungu, Dean Furman, Keagan Dolly and Kamohelo Mokotjo among others.
However, he has decided to call-up the likes of Tiyani Mabunda and Thulani Serero to boost his midfield for the crucial clash set for the FNB Stadium where both teams are targeting the full three points.
"So, I believe that the players won't have a problem, with not wanting it enough and not being able to balance that mental attitude towards the game," he continued.
"Secondly, it doesn't matter if we've got a lot of injuries. I would love to have some of those (injured) players in the game, but we've got to get on with it,” responded the English mentor.
"I think the (current squad) players would do just that. I think they'll quickly understand their roles and I think they will quickly make sure that they give a performance," concluded Baxter.