"Rojas has been granted an amnesty," said Andreas Herren, a spokesman for soccer's ruling body. "It takes effect immediately."
The request for a pardon was made on Rojas' behalf by the Chilean players' union.
Rojas now works as a trainer in Sao Paulo, Brazil.
Rojas fell in the penalty area during a game against Brazil.
He contended he had been hurt by a signal flare thrown from the stands.
The Chilean team walked off in protest, and the game at Maracana Stadium was halted.
But subsequent investigations showed that Rojas had deliberately cut himself in an attempt to stop play. Brazil was leading 1-0 at the time.
FIFA banned Rojas for life, along with coach Orlando Aravena and team doctor Daniel Rodriguez.
A Chilean inquiry found that Aravena ordered Rojas by walkie-talkie to remain on the ground leave the field a stretcher.
Rodriguez was accused of submitting a fraudulent medical certificate.
Team co-captain Fernando Astengo was disqualified from national or international soccer play for five years for deciding to pull the team from the field.
The Chilean national team also was barred from the 1994 World Cup.