The Inter team, and coach Andrea Stramaccioni, declared a media silence after the stoppage-time incident.
"I can say that for three games in a row, we have had to deal with refereeing injustices, which have prevented us from getting the result," Moratti told Mediaset.
"I cannot stay quiet in these circumstances," he said from the seat of his car after stopping to talk to reporters on the way out of San Siro. "That penalty was as big as a house.
"I don't think there's any plot against us, it's just that referees are incapable of doing their jobs."
Inter were furious after an alleged foul on Andrea Ranocchia in the penalty area failed to bring a spot kick and Stramaccioni was sent off as he led the Inter protests on the pitch.
In their previous game, Inter were angry over a penalty awarded to Atalanta who went on to win 3-2.
In the match before that, the Milan side claimed that a Juventus goal against them was scored from an offside position, although Inter eventually won 3-1.
"Some commentators like to amuse themselves by pretending it wasn't a penalty, but if that's not a spot-kick then I don't know what is," added Moratti.