As many as 200 fans forced entry into the media centre and other areas of the ground an hour before kick-off, raising major security concerns for FIFA and tournament organisers.
Eyewitnesses, including a number of British journalists, said they charged through a security checkpoint before smashing down a glass door and invading a working room.
Police were called to the scene and stadium security were able to reprimand and hold 30 Chile supporters, while others managed to escape the stadium after failing to gain entry to an area in which to watch the game.
A FIFA statement released on Wednesday confirmed: "Ahead of the Spain-Chile match at the Maracana, a group of individuals without tickets violently forced entry into the stadium, breaking fences and overrunning security.
"They were contained by the security and did not make it to the seats. The situation was brought under control quickly and at least 85 intruders were detained according the military police of Rio de Janeiro.
"The organisers of the FIFA World Cup condemn these acts of violence and we will communicate further information and measures to be taken in due course."
Maracana security guard Diego Guilhermede Souza Goncalves said: "They stormed the gate and ran into the stadium but we stopped them."
Chile knocked reigning World Champions Spain out of the tournement with a 2-0 victory on the night, and joined Netherland on six points in their group, with both sides having beaten Australia.