Guerrero was banned for 14 months by the Court of Arbitration for Sport (CAS) in May, which would have kept him out of the World Cup, after testing positive for a cocaine byproduct contained in a tea he drank.
The 34-year-old, who has denied wrongdoing, appealed to the Swiss Federal Court, the final part of the sporting judicial system, which on May 31 agreed to lift the suspension pending a final decision.
Peru, playing at their first World Cup for 36 years, were eliminated in the group stage, although Guerrero scored when they beat Australia 2-0 in their final game.
FIFA said in a statement that it had taken note of the Swiss court's decision "to lift the provisional suspensive effect that had been granted with respect to the sanction imposed by CAS on the player Paolo Guerrero".
"Therefore the suspension imposed by CAS is in place," it added.
The Swiss Federal Court did not reply to a request for comment.
Guerrero, who plays for Brazilian club Internacional, tested positive for benzoylecgonine, a metabolite of cocaine, following a World Cup qualifier away to Argentina in October.
He was initially given a 12-month ban by FIFA, starting in November, which ruled him out of the World Cup. That was reduced to six months on appeal, putting him back in the tournament.
However, CAS increased the ban to 14 months, again ruling him out of the finals, following an appeal by the World Anti-Doping Agency (WADA) which considered six months to be too lenient.
Guerrero has said the substance was found in his system because of a herbal infusion he drank that was contaminated with coca leaf, an ingredient in cocaine which is also widely used as a non-narcotic traditional remedy in South America.
CAS recognised that Guerrero ingested the substance unknowingly and did not intend to enhance his performance.
(Reporting by Brian Homewood, editing by Ed Osmond)
