Blatter, who also promised that world soccer's governing body would step up its fight against drug cheats in the sport, said he had spoken to Palios and told him he was "happy he had reacted the way he had done".
Earlier, in his opening address, Blatter had referred several times to the recent controversy in England where defender Ferdinand was left out of the national squad after failing to attend a mandatory drugs test.
The Manchester United player, who was tested two days later and found to be negative, said he forgot to have the test.
Blatter told reporters Palios had congratulated the FIFA president on the success of the Extraordinary Congress on Sunday and he had, in turn, congratulated Palios "on the way, the week before, he had dealt with the national players."
Blatter added: "I was very happy he reacted this way. We need understanding and respect for our institutions in football and proper discipline and respect is very important. It is paramount for the future."
The England players threatened to strike and boycott their European Championship qualifying decider against Turkey on October 11, but they later backed down and played out a goalless draw that saw the team reach next year's finals in Portugal.
Blatter said their actions were deplorable and warned that "one doping case would be one too many. We must keep our sport clean".
Palios said leaving Ferdinand out of the England squad was a "policy decision" and said the outcome of the case against Ferdinand would only be known when all the due and necessary procedures had been completed.
He declined to comment further after learning of Blatter's praise for his position in the dispute with the England players.
During the Congress, neurologist professor Jiri Dvorak reported that FIFA had recorded only one positive dope test out of 2,390 taken at its competitions since 1994.
The positive test was taken by Diego Maradona of Argentina during the 1994 World Cup finals in the United States.
Blatter praised the clean bill of health from all 32 teams at the 2002 World Cup finals and other tournaments but warned FIFA did not agree with World Anti-Doping Association (WADA) demands for a mandatory two-year suspension in all cases.
He said he did not believe FIFA or other sports federations should be dictated to by a quasi-political organisation that was 50 percent funded by national governments.
Blatter said he would invite WADA to join FIFA at a meeting of the Team Sports Federation later this year, adding that 70 percent of people active in sport are represented by teams and do not participate as individuals.
Blatter said that in future FIFA would strive to avoid situations where players might be dope tested twice by two different organisations at the same match.
He said this was a matter for communication and organisation and would be part of FIFA's pursuit of an acceptable world standard for anti-doping practices in sport.