The seven-times European champions crashed out of the competition after a 5-1 aggregate loss to Atletico Madrid, who humbled the Italian giants 4-1 in the last-16 second-leg tie on Tuesday night.
The Gazzetta dello Sport was critical of Balotelli after the Italy international failed to make any impact over both legs.
"Balotelli remains switched off," read one Gazzetta headline.
The Corriere dello Sport said: "Terrible performance by the Rossoneri.
"Kaka goal, Balotelli disaster."
Tuesday's result was the latest setback for a Milan side that have endured a dismal campaign and are 38 points behind Serie A leaders Juventus.
Clarence Seedorf, who took the Milan reins in January following the sacking of coach Massimiliano Allegri, has also come under fire.
Gazzetta's editorial questioned Seedorf's tactics and Balotelli's attitude. It said: "Balotelli and Seedorf are also under scrutiny."
The Rossoneri are 10th in the standings and in danger of missing out on European football next season.
The Gazzetta's top headline read: "Zero Milan, beaten and out of everything."
Turin-based sport newspaper Tuttosport highlighted that Milan's current troubles stem from their failure to sufficiently strengthen their team.
Their headline read: "Atletico too much for this Milan.
"Goodbye Champions League."
All three of Italy's major sports papers question the future of the club.
"What now?" asked Gazzetta.