The 77-year-old described the Portuguese as being "like a commander on the pitch" and joked he spent more money on his hairstyle than Barcelona rival Lionel Messi in an audience with Oxford University students last week.
“Football is about the difference between stars,” Blatter said.
“Lionel Messi is a good boy that every father, every mother would like to have at home.
“He is very quick, he is not exuberant, he plays well, he is a good boy. That is what makes him so popular, because he is this nice man and that is why he gets votes.
“The other one [Ronaldo], he is something else, he is like a commander on the field of play. This is the other side of football and it is good to have such commanders on the field also. That gives life to football.
“One has more expenses for the hairdresser than the other, but that doesn’t matter.”
Blatter’s comments have been met with fury in Madrid as Ronaldo aims to topple Messi to win the Ballon d'Or for the first time in five years after both men were nominated in the 23-man shortlist for the award.
"It seems to me like a lack of respect,” Real Madrid coach Carlo Ancelotti said in a press conference on Tuesday.
"I haven't spoken with Cristiano about it. He is serious, professional and respects everyone.
"I know that our president has sent a letter to Fifa."
But it was the Fifa president’s concluding comments that have led some critics to comment on the neutrality of the upcoming Ballon d’Or Awards.
“I cannot say who is the best,” Blatter began by saying.
“I like both of them, but I prefer Messi.”
Although Blatter’s words may have convinced some Real Madrid fans Fifa as a whole is biased towards Barça, Spanish football expert Sid Lowe sent out the following tweet:
"Lots of people saying Blatter anti-RMadrid for comments on Messi/Ronaldo. Blatter is an honorary member of RM and self-declared RM fan."
On a slightly more official note, French magazine France Football published on Tuesday the names of 23 footballers who are in the running for the prestigious 2013 Ballon d’Or award for the best footballer in the world.
The list will be whittled down to three names on December 9th with the winner being announced on January 13th in Zurich.
The full list of 23 players is as follows:
Gareth Bale (Real Madrid)
Edinson Cavani (Paris-SG)
Radamel Falcao (Monaco)
Eden Hazard (Chelsea)
Zlatan Ibrahimovic (Paris-SG)
Andrés Iniesta (Barcelona)
Philipp Lahm (Bayern Munich)
Robert Lewandowski (Borussia Dortmund)
Lionel Messi (Barcelona)
Thomas Müller (Bayern Munich)
Manuel Neuer (Bayern Munich)
Mesut Özil (Arsenal)
Andrea Pirlo (Juventus Turin)
Franck Ribery (Bayern Munich)
Arjen Robben (Bayern Munich)
Cristiano Ronaldo (Real Madrid)
Bastian Schweinsteiger (Bayern Munich)
Luis Suarez (Liverpool)
Thiago Silva (Paris-SG)
Yaya Touré (Manchester City)
Robin van Persie (Manchester United)