Balotelli was dropped for the clash against Napoli, with Mourinho questioning his dedication.
In an interview with Corriere dello Sport, Moratti said: "Mourinho's telling off was made with affection - it was serious and professional.
"Balotelli is an intelligent lad and I'm sure he will understand the situation.
"We are going through a good period and the sides around us have been struggling a little," Moratti enthused.
"I am pleased with the way we have been playing and this gives everyone belief."