Ukraine's supporters were involved in "several racist and discriminatory incidents" during the 9-0 win over San Marino in a qualifier in Lviv on September 6, added the world governing body.
The FARE (Football Against Racism Europe) observer at the match reported that local fans displayed neo-Nazi banners and made "monkey noises and gestures" as well as Nazi salutes.
Ukraine, who host Poland on Oct. 11 before their last qualifier away to San Marino, are second in Group H on 15 points, level with Montenegro and one behind leaders England. Poland are fourth with 13 points.
Ukraine, whose supporters set off fireworks at the San Marino game, have also been banned from playing any qualifiers for the 2018 World Cup in Russia at the Lviv Arena.
In addition, FIFA's disciplinary committee fined the Ukraine Football Federation (FFU) 45,000 Swiss francs (£30,750).
Peru, who are already out of the running for a place at the 2014 finals in Brazil, must play their next home World Cup qualifier against Bolivia on October 15 without any fans.
The sanctions, which also included fining the Peruvian FA (FPF) 20,000 Swiss francs (£13,500), were imposed by FIFA after crowd disturbances during the 2-1 qualifying defeat by Uruguay in Lima on September 6.
FIFA said if such incidents occurred again it would have no option but to impose harsher sanctions against the Ukraine and Peru federations which could include "a match forfeit, a points deduction or disqualification from a competition".
- Sports & Recreation
- San Marino