Earlier this year, Chile were handed a two-match ban, with one suspended for the same offence.
Having already played one game away from their national stadium in Santiago, they will now have to find a new venue for their World Cup qualifying match against Venezuela next March, world soccer's governing body said.
FIFA triggered Chile's suspended sentence following their World Cup qualifier against Bolivia in September.
"Since Chile had committed another infringement during the probation period imposed in May 2016, a ban on playing at the Estadio Nacional Julio Martinez Pradanos in Santiago for a further match will be applied," FIFA said in a statement.
Chile were fined a total of 65,000 Swiss francs ($66,421) for two offences after their fans were also found guilty of "insulting chants" in September's clash against Paraguay.
Chile are seventh in the South American World Cup qualifying group with 11 points from eight games, two points outside the top four spots which guarantee a place at the finals in Russia.
FIFA also handed out fines for homophobic chanting by supporters to Honduras (65,000 Swiss francs), El Salvador (45,000), Mexico (30,000), Peru (30,000) and Brazil (20,000).
Italy, Argentina, Canada, Paraguay and Albania were fined between 20,000 and 50,000 Swiss francs for "incidents involving discriminatory and unsporting conduct by fans".
($1 = 0.9786 Swiss francs)
(Reporting by Toby Davis in London; Editing by Ken Ferris)
