He released a statement saying the former South Africa president was "probably one of the greatest humanists of our time."
Blatter said he and Mandela "shared an unwavering belief in the extraordinary power of football to unite people in peace and friendship."
One of Mandela's last major public appearances was during the closing ceremony of the 2010 South Africa World Cup.
Blatter is in Brazil for Friday's World Cup draw that determines who and where the 32 nations will play next year.
FIFA's president said the flags of the 209 member associations at FIFA's headquarters will be flown at half-mast and there will be a minute's silence before the next round of international matches.