Guerrero tested positive for a stimulant after the Argentina-Peru match on Oct. 5 and was given a preliminary 30-day suspension, the Peruvian Football Federation said on Friday.
The ban means he is almost certain to miss the first leg against New Zealand in Wellington on Nov. 11 and the return match in Lima four days later. The winner of the tie will secure a place in next year's World Cup Finals in Russia.
"At the national team, we are aware of what anti-doping control is," doctor Julio Segura told Peru's Radio Nacional late on Friday. "So we don't use any substances that produce doping (results). It's a shame what happened with Paolo but I am sure there was no problem from our side."
The ban is a huge blow to Peru, who are hoping to reach the World Cup Finals for the first time since 1982.
Guerrero, 33, is the team captain and talisman, with his 32 goals in 83 appearances one of the main reasons the South American side are so close to a fifth finals appearance.
His suspension has provoked consternation in Peru, with even the country's president weighing in.
"This seems terrible to me (that he will miss the playoffs) but first and foremost we have to understand what happened," Pedro Pablo Kuczynski told local radio station RPP.
"Everyone in Lima takes some kind of anti-histamine because of the awful climate here in winter," Kuczynski said. "Maybe he took an anti-histamine and it would be unfair if he was punished for that.
"However, we are going to look at the facts and I hope they are favourable and that he can play, because right now he's out."
(This story corrects date in paragragh 2 to make clear match took place on Oct, 5 and not Oct. 15)
(Reporting by Andrew Downie; additional reporting by Ursula Scollo; editing by Clare Fallon)
