FIFA president Sepp Blatter
FIFA says it allowed UEFA's request to keep the former warring neighbors apart when qualifying groups are drawn July 30 in Rio de Janeiro, Brazil.
The teams were also kept separate in UEFA's 2012 European Championship qualifiers.
Armenia and Azerbaijan, which have no diplomatic relations, were drawn together in Euro 2008 qualifying but the matches were never played. The countries are in dispute over the Nagorno-Karabakh territory.
Russia and Georgia briefly warred in August 2008.
FIFA says UEFA was the only one of its six continental confederations to make special requests.