The 34-year-old was dramatically hauled off the pitch after he alleged a fourth official bungled a substitution, pulling Neymar instead of teammate Gonzalo Escobar despite the forward only leaving temporarily for treatment on his calf.
The fourth official raised the board with his number 10 displayed as Robinho Jr took his place. But as Neymar tried to return to the field, he received a yellow card before getting involved in a furious protest.
The referee refused to entertain his arguments and in a moment of desperation, Neymar snatched the substitution slip from the officials and showed it to a TV camera to prove Escobar was meant to come off, not him.
"The fourth official got the substitution wrong," Santos said in a post on X.
"This was confirmed by the television coverage and by the note used by the officials during the substitution. An inexplicable error that was not corrected."
The mix-up could not have come at a worse time for Neymar, with Brazil coach Carlo Ancelotti set to announce his World Cup squad on Monday.
The Italian has said Neymar's inclusion will be based on fitness and form, not sentiment. He has six goals and four assists for Santos across all competitions this season.
Despite being Brazil's all-time top scorer with 79 goals, Neymar has not played for his country since 2023 due to injuries and a knee surgery that kept him sidelined for a year.
The frustrated forward eventually left the field and handed the captain's armband to Escobar, the very player who should have been substituted in the first place.