Dorival had banned the 18-year-old who enraged the coach by questioning why he was not chosen to take a penalty after being brought down in last week's 4-2 home win over Goianense in the Brazilian championship.
"Dorival Junior is no longer coach of Santos Football Club. The team will be coached in an interim capacity by Marcelo Martelote in the 'clasico' against Corinthians," Santos said in a statement on Wednesday.
The club's board was unhappy with Dorival's decision to extend Neymar's ban to a second match after he missed Sunday's 0-0 home draw against Guarani.
The supremely gifted Neymar, who English champions Chelsea courted in July and August, sparked a free-for-all at the end of Santos's previous match at Ceara, a 2-1 defeat, by arguing with an opponent over his close marking.
Dorival, who took charge at the beginning of this season, had a contract until the end of next year. He was in charge for 61 matches with 37 wins and 16 defeats.
He steered Santos to victory in the Paulista (Sao Paulo) state championship and Copa Brasil in the first half of the season. They are sixth in the Brazilian championship standings.
