Neymar did not feature for Santos in Sunday's 2-1 semifinal defeat at Corinthians because of ongoing "discomfort" in his left thigh.
The Brazilian forward picked up a muscular problem in last week's 2-0 win against Bragantino and had to watch from the bench as his team was eliminated from the Campeonato Paulista.
"All I wanted was to be on the field today and help my teammates in some way," a disappointed Neymar wrote on Instagram. "But last week, I felt discomfort and that prevented me from being on the field today. We did a test this morning and I ended up feeling it again!
"Unfortunately, it's part of football ... It didn't work out today, but we'll come back even stronger to fight for our goals!"
Neymar, 33, was recently named in Brazil's squad for the upcoming World Cup qualifiers against Colombia and at Argentina.
He has not featured for Brazil since October 2023, when he tore the ACL and meniscus in his left knee while on international duty.
Santos coach Pedro Caixinha denied reports that Neymar rested on Sunday in view of Brazil's upcoming games.
He said: "The only thing that we considered was that the player has discomfort, if he has discomfort, I'm not going to risk the player at Santos'. I'm not thinking about the Brazilian national team. When a player has discomfort and it could be associated with some risk of injury, I'm not going to take a risk.
"One of the things we have promised is we will do everything we can to ensure that Neymar does not get injured. Discomfort is not an injury. We are not going to make a case where it does not exist, just because he felt discomfort and was not in a position to give his best.
"It was my request, and he agreed to be with the group even though he knew he wouldn't be able to play, because he's a different, enlightened player, who has fantastic energy, and he suffered a lot for not being able to participate in the game."
Neymar is Brazil's all-time leading scorer with 79 goals.
Brazil host Colombia in Brasilia on March 20 before facing world champions Argentina in Buenos Aires five days later.