The Brazil international played and scored in the midweek Coupe de la Ligue victory over Amiens, but he will not travel to the Stade de la Beaujoire.
A rib injury has reportedly sidelined the 25 year-old, although PSG manager Unai Emery offered little suggestion of a fitness problem for the star striker in his pre-match media conference.
"We are preparing for the match against Nantes with the entire squad," Emery said. "Edinson Cavani and Javier Pastore will rejoin the squad when they have caught up the training days they missed.
"We have two more sessions ahead of Sunday's match. We will see how the players recover from the Amiens match. I think everybody should be fine.
"Only Thiago Motta is working individually to come back from injury."
However, when the travelling squad was confirmed by PSG later on Saturday, Neymar was a notable absentee – along with Pastore.