Goals from Sergio Ramos, Arjen Robben and Gonzalo Higuain gave Los Merengues the win in a game where Osasuna were denied two clear penalties by the referee.
The game also witnessed the sending off of Osasuna's Juanfran, who according to the arbitrator was simulating to win a spot-kick.
"I believe that the referee has hurt Osasuna, but sometimes, that happens to us too,” Mijatovic told Real Madrid's official website.
"However, we were deserved winners. We played a great second half and despite the injuries, the team still went all out, even after going a goal down."
Osasuna anger
From his side, Osasuna president Patxi Izco hit out at the referee, saying that what happened during the game is forcing the board to break their silence.
"Osasuna has always tried to maintain a positive relationship with the referees, because we feel it is the best thing to do, but yesterday, it went too far," said Patxi.
"I believe that we have every reason to do this; it has been recognized by everyone as a scandal. We know it is not a positive change but one day it has to stop."
Patxi added that similar decisions played a big role in demoting the club into the bottom of La Liga table.
"What happened yesterday is the current news but we cannot forget the refereeing that happened in Sevilla, Mallorca, Valencia, and in the way we lost to Sporting Gijón.
"This is the final straw," the angry president concluded.