The 33-year-old, who has experienced a challenging return to his childhood club this year, approached the stands at the conclusion of the match to Internacional discuss with a fan who seemed to be expressing discontent.
Footage revealed Neymar visibly upset and gesturing, then giving a thumbs up as a teammate encourages him to leave.
Santos had been striving to recover from a two-goal deficit, with Alvaro Martin Barreal netting one minute into stoppage time. Three minutes later, Neymar believed he had scored with a left-footed strike and celebrated in front of enthusiastic home supporters.
However, disapproval echoed throughout Vila Belmiro stadium as the referee determined that the ball had not fully crossed the goal line.
Santos currently sits 17th in the 20-team league, where the bottom four teams will be relegated to Serie B at the end of the season.
The former Barcelona and Paris Saint-Germain player has faced numerous difficulties since his return: sidelined by injury, receiving a red card for a handball, and contracting COVID-19.