Baxter remains head coach of SuperSport United until the end of the season, but will not oversee the team for their CAF Confederation Cup tie with Gabonese outfit FC Mounana in Libreville on Tuesday.
Baxter's assistant Kaitano Tembo will be in charge for that game, with Baxter returning to manage Matsatsantsa's final league match of 2016/17 with Platinum Stars at Lucas Moripe Stadium on Saturday.
The Brit, who is spending the week at Safa House and will name his Bafana squad on Thursday, will conclude his club duties with the Nedbank Cup final against Orlando Pirates on June 24.
"I'll not be in Gabon. I'll be at Safa House this week doing my preparing for the Nigeria game. I've done work on the squad, I've done some work on the opponents and I'm reading Nigerian news every day, trying to find out what they are thinking," said Baxter.
"I'll try to pick a team with a few warriors that will take us to Nigeria to get us the results."
Bafana last met Nigeria in 2014, playing to a 2-2 draw which dashed the West African nation's hopes of defending their continental title at the 2015 Afcon.
Baxter says he will be assessing the Super Eagles' recent performances.
"I'll have to be 100 percent honest, I haven't had time because of my commitments here at SuperSport. I haven't time I have to say," he said.
"The next two days I'll take my SuperSport hat off and put my Bafana hat on. It's not perfect and the preparation will not be perfect.
"But I'll get the DVDs, I'll break that down of their last three games. We played them a 2-2 game, I saw that and I'll get that, I'll break that down, so we'll do some preparation.
"But I think the important thing is to get the squad right, get the right sort of squad."
Baxter previously coached Bafana from May 2004 to November 2005, winning 10 of 23 matches before being fired after South Africa missed out on the 2006 World Cup.