The FA did not take retrospective action against the Manchester United striker, claiming FIFA rules prohibited it because referee Mark Clattenburg had taken action in the match, awarding a free-kick against Rooney.
But Blatter said: "This is up to the discretion of the national association. They can use video evidence in the discipline and control committee.
"They can impose or change a decision if a red or yellow card has been given to the wrong player. If there's violence the national association can intervene and punish a player - this is permitted at the discretion of the national association."
Blatter was speaking at a news conference on Saturday following a meeting of the International FA Board, the game's law-making body, but FA chairman David Bernstein - who was seated next to the FIFA president - insisted they had followed FIFA's rules.
He also claimed that only really serious incidents such as Ben Thatcher's forearm smash on Pedro Mendes in 2006 could be deemed "exceptional".
Bernstein said: "In the Wayne Rooney situation, under FIFA regulations if the referee sees the incident - which in this case he did do, the FA has no authority except in what is called exceptional circumstances, really exceptional - the Ben Thatcher incident is the only one where that has been used.
"If you open the door to 'halfway exceptional' the floodgates will open. I think that has more merit than meets the eye, the basis of the primacy of the referee staying in place - even though that will upset fans sometimes and quite understandably."
Bernstein said he believed Blatter may not have understood the Rooney incident "as clearly as it was".
He added: "I'm very clear that my view is correct. I've been properly advised on this. If the referee states he has seen the incident the FA is not able to make decisions except in exceptional circumstances."
Thatcher received an eight-match ban suspension after the then Manchester City defender fractured Portsmouth midfielder Mendes' skull.
FIFA's rule 77 states "sanctioning serious infringement which have escaped the match officials' attention" and national associations can rectify "obvious errors in the referee's disciplinary decisions".
Meanwhile, Blatter called on managers to show more respect to referees after he was asked about Manchester United boss Sir Alex Ferguson questioning the integrity of official Martin Atkinson.
Blatter said: "Everyone deserves fair play. Respect starts with self-discipline. This is what we are asking everywhere, from youth teams upwards and it is also valid for personalities.
"The higher your position the higher your responsibility. Those that have more power should be more responsible towards others. This is a principle in life."