Colombia defender Juan Zuniga kneed the 22-year-old Neymar in a crunching tackle and the Barcelona player was stretchered off in agony in the closing minutes of the game in Forteleza.
The injury and the suspension of captain Thiago Silva for the semi-final against Germany overshadowed a sensational David Luiz goal that sealed victory in one of the most physical games seen at this World Cup.
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Brazil coach Luiz Felipe Scolari fumed that Neymar has been "hunted" throughout the tournament and that no punishment was given for the tackle on him.
"I have been saying for three matches that Neymar has been hunted, but all the other countries say it is not true and it is only their players that are hunted."
Silva was booked for a second time in the tournament for impeding a clearance by Colombian goalkeeper David Ospina.
But in Zuniga's case "there was not even a yellow card and Thiago got a yellow card for nothing," Scolari said.
Brazil are in the World Cup semi-finals for the first time in 12 years, but Scolari, who has vowed his side will win their sixth World Cup, now faces a major crisis.
Silva put Brazil ahead after seven minutes and Luiz scored a sensational 30 metre free kick to give Brazil victory.
Colombia's James Rodriguez extended his lead as the tournament's top scorer with his sixth goal in five games from the penalty spot after Julio Cesar brought down Carlos Bacca.
But Colombia now leave and Brazil must now prepare without Neymar and key defender Silva for only their second World Cup meeting with Germany in Belo Horizonte on Tuesday. The Germans beat France 1-0 earlier in the day.
Luiz's goal was another special moment in the World Cup.
"Today It was great because I hit the exact point where the ball can go many ways and it is difficult for the goalkeeper," said Luiz.
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