The Spain forward scored Barca’s equaliser on 56 minutes after sprinting ahead of Fabio Coentrao, but replays suggested that he may have strayed fractionally offside in the buildup.
"The first goal for Barcelona was a big mistake by the linesman, and that is it," declared Mourinho to reporters after the match.
"I decided not to talk about certain decisions this season, but you know what I mean."
And he later told AS: "I don't want to criticise vital decisions all season, even less so in the second game."
The Portuguese trainer also expressed his thoughts on his team’s performance, while reserving words of praise for winger Jose Callejon.
“I did not like our first half, but in the second half, it was a different game.
“Callejon played well. He prepared the game for Di Maria. This was an important game and I liked his work,”
The second leg of the Supercopa is set to be played at Santago Bernabeu in six days’ time, but both sides will be in action in La Liga over the weekend, with Madrid facing Getafe and Barcelona taking on Osasuna.