FIFA said on Thursday the ban had been lifted under the so-called "suspensive effect" after Ukraine appealed.
It added there was not enough time for the appeals committee to hear the case before the match on Oct. 11.
A similar ban on Peru supporters for their home qualifier against Bolivia on October 15 was also lifted pending appeal.
"Only once the FIFA appeals committee has had an opportunity to decide on the appeals will FIFA communicate further information on the two cases," world soccer's ruling body said in a statement.
In Peru's case the appeal could backfire because they may have to play a more important game behind closed doors.
Peru and Bolivia have both been eliminated, making their match effectively a friendly.
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, FIFA said.
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 ahead of their last qualifier in San Marino, are second in Group H on 15 points, level with Montenegro and one behind leaders England.
Poland are fourth with 13 points.
Peru were initially sanctioned for crowd disturbances in their 2-1 home defeat by Uruguay on Sept. 6.