Three players had gone missing on Thursday in Toronto prior to their team's match against Canada a day later which the hosts won 3-0.
"FIFA can confirm that three players defected already last Thursday, leaving the Cuban team with 11 players in the squad for the qualifier against Canada," FIFA said in a statement.
There is a history of Cuban athletes defecting to pursue a potentially lucrative professional career outside communist-run Cuba. Seven members of Cuba's Olympic team defected in Florida in 2008 after a game against the United States.
In March, a Cuban player left his team while they were in Tennessee for an Olympic qualifying tournament.