The 34-year-old was sent off following an altercation with Bahia midfielder Rodrigo Nestor, and the sports tribunal found him guilty of violating the Vinicius Jr. rule that forbids players from covering their mouths during on-field confrontations.
The STJD said the referee's report also noted that Neymar, after being sent off, ran towards the visitors' bench to confront his opponent and had to be restrained by teammates.
The suspension means Neymar will miss Santos' next three matches. He is already banned for Wednesday's league game against Palmeiras after accumulating three yellow cards and will serve two additional matches for the protocol violation.
Neymar and Santos can appeal the ruling regarding the violation.
The latest suspension comes three months after Neymar became the first player in Brazil's top flight to be temporarily removed from the field under a new rule being tested in the league to curb time-wasting by goalkeepers.
The former Brazil captain is not expected to return to action until late November.