Born in Athens, Karnezis started his professional football career at Panathinaikos in 2007. He counted only a few appearances for the club until the 2011-12 season, when he got more chances and impressed. So, after a few months, his coach, Jesualdo Ferreira, trained him and he made him the regular goalkeeper of Panathinaikos F.C. He gave great performances and he saved his team at crucial moments.
His good performances led Greece national football team coach Fernando Santos to call him for a friendly match on 29 February 2012 against Belgium, in which he made his international debut, playing the entire game. Unfortunately for Karnezis, Fernando Santos didn't call him for Euro 2012 to be one of the three goalkeepers of the Greek National Team. Fernando Santos said: "If Karnezis keeps going that way, he will be without a doubt in the squad of the Greek National Team for the qualifying matches of Mundial 2014." And, indeed, he was called to be part of Greek National Team both for a friendly game with Norway and for the qualifying matches after that.