The Brazilian broke the deadlock in the 24th minute in Skopje, slotting Dani Carvajal’s long pass into the bottom corner of David de Gea’s net.
Replays show he had strayed fractionally offside, but the goal was allowed to stand. Isco doubled Madrid’s lead, before Romelu Lukaku pulled one back for Mourinho’s men.
“I think we did well, I think we lost to one goal which shows the result was really short and one of their goals was an offside. With a good VAR system it would be 1-1 and extra time,” Mourinho told BT Sport.
“They could have scored more goals than they did, we could have scored more goals than we did. They had a period of dominance at middle of the first half and we had a period of dominance at middle of the second half.”