In addition, he warned clubs they risk forfeiting matches if there is any repeat.
Former Portsmouth and Tottenham player Boateng led his team-mates off the pitch during a match at Pro Patria after being subjected to racist chanting from a section of the home fans, with the former Ghana international insisting he would walk off again in any competitive match under similar circumstances.
Speaking at a conference in the Middle East, Blatter said football must take a "zero tolerance" approach to racism but suggested that clubs should have to forfeit matches if their players force the abandonment of a match, whatever the reason.
Quoted in United Arab Emirates newspaper The National, he said: "Walk off? No. I don't think that is the solution.
"But the Italian federation has yet to provide FIFA with a report detailing what exactly has happened.
"I don't think you can run away, because then the team should have to forfeit the match. This issue is a very touchy subject, but I repeat there is zero tolerance of racism in the stadium, we have to go against that.
"The only solution is to be very harsh with the sanctions (against racism) - and the sanctions must be a deduction of points or something similar."
He added: "We have to have no tolerance to racism, absolutely no tolerance.
"This action is an example that the spectators must behave well because, as I understand it, the player ran away and the others went with him. (The spectators) cannot go on abusing afterwards."
In an interview with CNN broadcast on Friday, Boateng expressed his frustration with a perceived lack of support from world football's governing body.
He added: "So many people in FIFA can do something and they should wake up and do it. They should not tolerate it. They should ban people forever from the stadiums. That's the first thing you can do."
The Italian Football Federation (FIGC) has responded to the incident by announcing it will conduct an investigation.
Milan's players wore anti-racism shirts in the warm-up prior to their Serie A match at home to Siena on Sunday, with club owner Silvio Berlusconi having backed Boateng's actions earlier this week.
Football Association general secretary Alex Horne believes players do have the right to walk off the pitch, but only if previous attempts to draw the abuse to the attention of the referee have been ignored.
"If players are receiving sustained abuse on the pitch they should be reporting it to the referee," Horne told BBC Radio Five Live's Sportsweek programme.
"The players, through the captain, should be reporting it to the referee. The referee should be taking the players off the pitch and warning the crowds that they should desist with their abuse, and ultimately there's a sanction there if the fans don't listen to that.
"If the players feel the referee isn't dealing with it then I can understand why they walk off the pitch. Why should you have to tolerate that in this day and age?"