Neymar was hurt in the 86th minute, falling to the ground in pain after Zuniga jumped into him from behind.
Brazil teammate Marcelo quickly called for medical assistance when he saw Neymar writhing in pain. Neymar stayed face down until team doctors arrived and put him on a stretcher.
"Everybody knew that Neymar would be hunted," Brazil coach Luiz Felipe Scolari said. "It's been happening in the last three matches and we had been talking about it. But nobody listens to us."
Friday's match ended with 54 fouls in total — 31 by Brazil and 23 by Colombia. Scolari said Spanish referee Carlos Velasco Carballo should have done more to take control of the match.
According to Hulk, another of Brazil's striker, Neymar needs more protection from the officials.
"Every time is like this. Players always come after Neymar," Hulk said. "The referees need to do more to keep this from happening."
Associated Press video journalist Renata Brito contributed to this report.
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