The striker turned villain late in the first leg of the semi-final when he was sent off for a second booking after a foul on Santos's Neymar and will miss the second leg in Sao Paulo next week.
Shortly after the red card, the referee removed a police helmet from the pitch that had apparently been thrown on by Santos fans close to Corinthians goalkeeper Cassio. TV showed police officers among the Santos fans after the incident.
The match at Vila Belmiro, where Santos were previously unbeaten in this season's competition, was also marred by a 20-minute delay after a floodlight failure in the 82nd minute.
Emerson took a pass from Paulinho inside the box with almost half-an-hour gone and hit a curling shot into the top far corner for the only goal.
Santos were unable to make their extra man pay in the last 13 minutes after Emerson's red card, exerting constant pressure but failing to create a clear-cut chance.
"The fight to the end, especially after Emerson's' dismissal, showed the spirit of this team," Cassio told TV reporters.
"We managed to do what was planned by the coach and now we're heading home with this result but always thinking of winning in front of our own fans."
Corinthians have never reached the final, while Santos are looking for their fourth title after winning their first two in the Pele era.
Santos, with the highest scoring attack in the competition, had won all their home matches until Wednesday when they encountered a strong Corinthians defence that has only conceded two goals in the tournament.
Neymar was unable to show off his dribbling skills as he was starved of the ball with Corinthians, putting 10 men behind the ball after their goal, cutting out Santos attacks at their genesis.
"From what I understand about football, only one team [Santos] played for the entire match, but Emerson scored with a lovely shot. Football's like that, it happens," a dejected Neymar said.
The winners of the tie will go through to a final against six times champions Boca Juniors or Universidad de Chile, who meet in the first leg of their semi-final at La Bombonera in Buenos Aires on Thursday.
