Guerrero tested positive for cocaine following a World Cup qualifier in Argentina in October after drinking a tea containing the substance, CAS said.
It accepted that Peru's all-time leading scorer did not intend to enhance performance but said he was at fault, even if not significantly.
The 34-year-old was initially banned for 12 months by FIFA, which was then reduced to six months on appeal. The suspension finished 10 days ago.
However, CAS partially accepted an appeal from the World Anti-Doping Agency (WADA) which had requested the sanction be increased to between one and two years.
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Guerrero, who has denied wrongdoing throughout, had also appealed to CAS to request the ban be annulled altogether.
"This is very hard for me," the player said in a recorded message broadcast on Peru's Canal N.
"Today I feel like my dreams, first of playing football and second of playing in a World Cup after 36 years, I feel like they're gone.
"This is a very dark hour, dark due to what I'm going through, but I want to reiterate to my country, to my people, that I have never taken any kind of drugs.
"To the people who've contributed to this shameful injustice (I say to them), you are stealing my World Cup and perhaps also my career. I hope you can sleep at night."
Guerrero had played two games for his Brazilian club Flamengo, scoring in Sunday's 3-2 defeat against Chapecoense in the Brazilian championship, between the end of his original ban and the CAS verdict on Monday.
Shortly before the decision, the Peruvian Football Federation (FPF) had tweeted a picture of Guerrero taking part in a photoshoot with the official team strip.
Guerrero's absence will be a significant blow for Peru who have qualified for their first World Cup in 36 years and face Denmark, France and Australia in their Group C.
He has scored 32 goals in 83 appearances and is a galvanising presence for his team.
The FPF said in a statement that it "profoundly regrets the lengthening of the ban imposed on our player Paolo Guerrero who has always shown exemplary conduct.
"We will without doubt miss Paolo in Russia but we are convinced that our team, with its courage and tenacity, will do Peru proud. No matter how tough the adversity, it will not stop our team."
Guerrero said he was now discussing what steps to take with his lawyers.
CAS said that Guerrero bore "some fault or negligence, even if it was not significant, and that he could have taken some measures to prevent him from committing an anti-doping violation."
Tea infused with coca leaves, which are used as the raw ingredient in cocaine, is popular in Andean countries and a traditional treatment for altitude sickness.
(Additional reporting by Andrew Downie, editing by Pritha Sarkar and Toby Chopra)
