They will forfeit the four points garnered from two games in September after fielding an ineligible Nelson Cabrera
Perennial South American makeweights Bolivia, whose only World Cup finals appearance came in 1994, beat Peru 2-0 in La Paz and then shared a goalless draw with Chile.
But they will now forfeit the four points garnered from those games in September after fielding Nelson Cabrera, who was ineligible.
Chile and Peru have been awarded 3-0 victories in both matches.
The extra points will benefit Chile primarily as they close to within a single point of Ecuador and Colombia, who currently fill the final two automatic qualifying positions for Russia 2018.
The Chileans notably leapfrog Argentina on goal difference.
A FIFA disciplinary committee also fined Bolivia 12,000 Swiss francs (11,000 euros or $12,300).
The Paraguay-born defender Cabrera came on from the bench in both games but had previously appeared for his country of birth in 2007.
Cabrera has spent only three seasons playing in Bolivia, short of the five needed for naturalisation, leading Chile to file a complaint to FIFA.