Guerrero was banned after testing positive for cocaine metabolite benzoylecgonine following Peru's World Cup qualifier with Argentina in October last year.
He appeared before the Court of Arbitration for Sport in Switzerland last week to appeal against the six-month ban and defend himself against a request for the suspension to be increased.
"I am very confident that it's going to be alright, because I am innocent," Guerrero said after the game.
"This is very emotional, a big crowd, the Maracana full, us winning 2-0," he added. "It's incredible living this after the six months I've gone through, this injustice."
Guerrero replaced centre forward Henrique Dorado in the 57th minute of Flamengo's league match against Internacional.
He almost scored with a free kick that flashed inches wide and the Rio club eventually won 2-0, a victory that lifted them two points clear at the top of the Serie A table.
Peru, who have qualified for the World Cup for the first time since 1982, will face Australia, Denmark and France and are counting on having their talismanic captain back.
Guerrero has scored 32 goals for his country and helped them finish third in the 2011 and 2015 Copa Americas when he was leading scorer in both tournaments.
(Reporting by Andrew Downie; Editing by Ian Ransom)
