The Spain international scored a fine second goal after Casemiro had put Madrid ahead in the first half, with Romelu Lukaku's strike not enough to prevent the European champions from claiming a 2-1 win in Skopje on Tuesday.
Isco's future had come under scrutiny in recent weeks, with the 25-year-old yet to extend a deal that expires next year despite insisting after last term's LaLiga title triumph that he would not be leaving.
However, speaking after the victory, Isco made it clear that he intends to stay at the Santiago Bernabeu.
"We're very close and it will be done soon," he said of the contract talks, as quoted by Mundo Deportivo.
Isco conceded that Madrid were put under some pressure by United in the closing stages but was in no doubt that they fully deserved to win a third Super Cup since 2014.
"The game overall was good, we were superior. We suffered a bit at the end against a powerful team," he said.
"They have great players and they started very well. They're a powerful side with big aspirations. But in general, we played a very complete game and we're deserving winners.
"We think of the present and the future. We don't usually fail on the big occasion. It's also because of the dressing room: getting along is much easier. We're building a winning group and we're showing that."