Argentina's Tigre refused to emerge for the second half after claims of police brutality, leaving Sao Paulo to pick up the trophy and heightening concerns over security for 2014.
The incident came moments after a brawl involving players and officials as the two teams left the pitch at half-time of the second-leg match.
"In football there are so many emotions and so much passion sometimes football cannot be controlled," Blatter told reporters in Tokyo after FIFA's executive committee meeting.
"But [after] such an incident, I have to say it also a warning for the organisers of the World Cup," he added 18 months before the tournament. "It's a warning for all organisers what can happen."
Accusations that a police officer had poked a revolver into the chest of goalkeeper Damian Albil was the latest in a series of controversies involving Brazilian police at matches.
Blatter said the responsibility for security at the World Cup lay with the organisers and local authorities and not with FIFA.
"Security is not a matter of the sports organisation," he said before Sunday's Club World Cup final between Chelsea and Brazil's Corinthians in Yokohama.
"Security is definitely a matter for the authorities, being the police, army or whatever. We have no power in football to go into the security.
"What we can do is give guidelines and can have a special security officer on spot but finally it is the organisation and responsibility of the police and army.
"It's a pity you can't play the second part of a match for any reason but it can happen in football."
"You have 300 million people around the globe playing this game or being involved in the game and it will be touched by the villains in our society.
"We are not the origin of violence. The origin of violence is in society. If you go back through history there was violence before football."
On a more positive note, Blatter praised the preparations being made by Russia for the 2018 World Cup after FIFA selected Moscow's Luzhniki Stadium for the tournament final.
"In February I will start my 38th year in FIFA," said the 76-year-old Swiss. "I have never seen preparation like for 2018 in Russia. The enthusiasm is so great."
Eleven Russian cities will host games at the 2018 World Cup, with Moscow having two venues.
"I was in Moscow when the decision was taken on the cities where the World Cup will be played," said Blatter. "It was like a fiesta in the cities, like they had won the World Cup."
