FIFA said on its website that its disciplinary committee fined Argentina's Racing, Independiente, Rosario Central and Instituto de Cordoba clubs, as well as Uruguay's Institucion Atletica Sud America.
FIFA accused the Argentine teams of acquiring players "through the Institucion Atletica Sud America for reasons unrelated to sports".
The moves, said FIFA, were designed to evade paying taxes by moving a player through a club in which he never actively plays for, such as is the case with Atletica Sud.
The so-called "bridge transfer" of players was uncovered by an investigation begun in 2012, which detected irregularities in six transactions involving the fined clubs.
"FIFA's disciplinary committee ruled the clubs acted in bad faith, since they had carried out the transfers for reasons having nothing to do with sports," the body said.
Instituto de Cordoba and Independiente took part in two "bridge transfers" and must now pay 50,000 Swiss francs (or just over $56,000), while Rosario Central was fined 20,000 francs and Racing 15,000 francs.
Sud America, meanwhile, was fined 40,000 francs and additionally banned from taking part in any national or international player transfers or sales for two seasons.