Chile were awarded a 3-0 win after FIFA's disciplinary committee ruled that Bolivia had fielded Nelson Cabrera when he was ineligible.
The decision took them up from seventh to fifth in the South American group and ahead of Argentina on goal difference. Both teams have 16 points from 10 games.
The top four teams qualify directly for the 2018 World Cup in Russia and the fifth enter a playoff against a side from another continent.
Peru, beaten 2-0 by Bolivia in La Paz in September, were also awarded a 3-0 win after Cabrera played against them as well. That win revived their faint hopes of a first World Cup appearance since 1982.
Bolivia were left with four points from 10 games, one place off the bottom of the 10-team group.
Brazil lead with 21 points followed by Uruguay (20) and Ecuador and Colombia (17).
Peru, in seventh place, have 11.
FIFA rules state the players can only play for an adopted country if they have lived and played there for five years.
Cabrera, born in Paraguay, moved to Bolivia four years ago to play for Bolivar.
Last week, the head of the Bolivian Football Federation (FBF), Rolando Lopez, said that FIFA's rules were "contradictory" and his federation had understood the period was two years.
(Editing by Ed Osmond)
