SAFA banned Serero from representing Bafana in February after he refused to report for national duty unless he was guaranteed game-time in Baxter's side for 2018 FIFA World Cup qualifiers against Senegal last year.
However, the national association have now lifted Serero's suspension.
Baxter has had to re-arrange his squad due to injuries to several of his key players – the latest being England-based Kamohelo Mokotjo.
Other influential men set to miss this fixture are Dean Furman, Bongani Zungu, Keagan Dolly, Sibusiso Vilakazi and Bradley Grobler, all out with long-term injuries.
“It has really been a tough task to select the team to face Nigeria without some of our regular players, but we have to soldier on. These injuries could not have come at the worst of times when we really need to collect all three points because we are well aware the importance of doing this,” said Baxter.
“The positive side, however, is that this gives us a chance to introduce other players into the squad, and these are players we have been monitoring, so it not like a knee-jerk reaction. This helps us to ensure that when we qualify for the tournament we have an even bigger pool of players to choose from. I am also confident that the players brought in will do a good job.”
Nigeria lead Group E with nine points, just one ahead of South Africa with two matches remaining.
Bafana will conclude their qualifying campaign with a trip to Libya in March.
“I must admit this makes the upcoming clash all the more interesting. Remember we beat them 2-0 in the first leg in their backyard, so they will come here trying to avenge that. On the other hand we want to regain the top spot which we relinquished with the draw away to Seychelles. The good thing is that qualification is still in our hands,” added Baxter.
Bafana are expected to assemble for camp on Sunday in Johannesburg. The match next Saturday at Soccer City is scheduled to kick off at 15h00.
The 2019 AFCON will take place from June 7 to 30 in Cameroon. The Indomitable Lions are the defending champions.
Goalkeepers: Itumeleng Khune (Kaizer Chiefs), Ronwen Williams (SuperSport United), Darren Keet (Bidvest Wits).
Defenders: Ramahlwe Mphahlele (Kaizer Chiefs), Motjeka Madisha (Sundowns), Siyanda Xulu (Maritzburg), Thulani Hlatshwayo (Wits), Innocent Maela (Pirates), S'fiso Hlanti(Wits), Buhle Mkhwanazi (Wits) Thamsanqa Mkhize (CT City).
Midfielders: Vincent Pule (Pirates), Lebohang Maboe (Sundowns), Hlompho Kekana (Sundowns), Fortune Makaringe (Maritzburg), Teboho Mokoena (SuperSport), Tiyani Mabunda (Sundowns), Thulani Serero (Vitesse), Thembinkosi Lorch (Pirates).
Strikers: Lebo Mothiba (Strasbourg), Percy Tau (Royal Union), Dino Ndlovu (Zhejiang), Themba Zwane (Mamelodi Sundowns).