Coach Dorival Junior had extended the controversial 18-year-old's suspension for indiscipline from his team into a second match, angering the club board who sacked him earlier in the day and reinstated Neymar.
However, Corinthians were too strong for Santos at their Vila Belmiro ground in the "clasico" and stayed three points ahead of second-placed Cruzeiro, who beat Ceara 2-0 at home in Belo Horizonte.
Neymar scored Santos' second goal to put them 2-1 in the opening half hour but Corinthians equalised through Elias and took the points with defender Paulo Andre's 70th-minute winner.
Former Brazil striker Ronaldo missed his fourth Corinthians match in row with a calf injury on his 34th birthday.
Corinthians have 47 points and a game in hand and Cruzeiro 44. Fluminense, who led the standings from July until their defeat by Corinthians last week, have 42 and can go second again if they beat Atletico Mineiro on Thursday.
Fourth-placed Botafogo, who have 30 points, recovered from two goals down for a 2-2 draw with Vasco da Gama in a Rio derby.
Botafogo pulled one back with a header by Argentine German Herrera before he was sent off for dissent and Uruguay striker Sebastian Abreu scored his second late penalty equaliser in successive matches.
DORIVAL OUT
Dorival, who steered Santos to the Paulista state championship and Copa Brasil titles in the first half of the season, had banned Neymar from Sunday's match against Guarani, a 0-0 draw and also wanted him to sit out Wednesday's game.
Neymar, a budding Brazil international, had enraged the coach by questioning why he was not chosen to take a penalty after he was fouled in last week's 4-2 home win over Atletico Goianiense.
The gifted teenager, 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 had been contracted to the end of 2011.
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