The Red Devils found themselves a goal down at Old Trafford in Saturday evening's clash and nearly conceded a second, before sparking into life and scoring four unanswered goals of their own to claim the victory.
Mourinho believes that trying to accommodate both Marcus Rashford and Anthony Martial in his starting lineup almost backfired, with both men popping up in similar areas, and admits that Newcastle arguably merited a half-time lead.
"They both like to play in the same position and that is difficult," he told reporters. "They both prefer to play on the left than the right, both playing with another striker through the middle; we lose a point of contact with the midfield that we are used to, with the player playing behind the striker.
"But we found then a certain balance and, when they started finding one opening on the left and one on the mid-left between the striker and the left winger, that was the moment where we start creating more. But, to be honest, Newcastle were probably the [better] team - not in the second-half, but in the first-half - and we felt a bit of instability in our defensive areas.
"That was clearly not because of the defensive players but because of our balance. To play them together gives us things but also takes some things from us."
United's 4-1 victory keeps them within eight points of Manchester City, whom they face on home soil in three weeks' time.