Bafana were on Thursday night drawn by CAF to battle the Super Eagles, Libya and Seychelles for a spot at Cameroon 2019.
The top teams in each pool qualify for the finals, along with the three best runners-up.
Bafana can draw encouragement from when they beat Nigeria to top spot in the qualifiers for the 2015 tournament in Equatorial Guinea.
"There was never going to be an easy draw but I am very happy with this one," said Jordaan, who attended the draw in the Gabonese capital of Libreville.
"It should be a direct shoot out between Bafana Bafana and Nigeria but I am confident that we should progress in this group."
South Africa, who have yet to appoint a new coach after the axing of Shakes Mashaba, travel to Nigeria first in the week of June 5-13, 2017.
They then take on Seychelles in home and away matches in the week of 3-11 September 2018, before a home clash with Nigeria between October 8-16 October, 2018.
The 1996 continental champions round out their pool campaign with an away tie against Libya on 5-13 November, 2018.