FIFPro says a 14-month ban barring the 34-year-old Guerrero from his World Cup debut is 'unfair and disproportionate'.
The 34-year-old had an initial one-year ban reduced to six months by Federation Internationale de Football Association and he returned to action for Brazilian club Flamengo earlier this month before being named in his country's provisional squad for their first World Cup since 1982.
Guerrero was subjected to an emotional roller-coaster after testing positive following the 0-0 draw in a qualifier away to Argentina in October.
The CAS chose to increase Mr Guerrero's suspension from 6 to 14 months, starting today, with the period of provisional suspension of 6 months already served by Mr Guerrero being credited against the total period of ineligibility to be served.
News of extension of the ban was not well received among Peru fans.
Guerrero's appeal against the ban was upheld.
"Both FIFA and the Court of Arbitration for Sport agreed Guerrero did not knowingly ingest the substance and that there was no performance-enhancing effect". A fan said that he had been looking forward to the World Cup, but with Guerrero's ban, there was nothing to be excited about anymore.
Guerrero has 32 goals for his country in 86 appearances.
But his solicitors argued that the drug was not a performance-enhancing substance and had been ingested accidentally, by means of "contaminated tea".
"However, the Panel considered that the Player did bear some fault or negligence, even if it was not significant, and that he could have taken some measures to prevent him from committing the [doping violations]".
"There is no reason for me to be suspended", he claimed after the match.
"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".
Bolivia fielded an ineligible player in a 2-0 win over Peru, and that result was overturned to a 3-0 loss by default.