Ferguson conceded he got his tactics all wrong after the 2-1 win.
His introduction of Nani and Ryan Giggs 13 minutes into the second half gave United the impetus and width that had been severely lacking.
While the history books will show a United victory, Ferguson admits his decisions left the side on the back foot from the offset.
"Sometimes we make it difficult for ourselves but, in fairness, I maybe meddled with the system somewhat this afternoon," he told MUTV.
"We tried a diamond in the middle of the pitch and, of course, Manchester United are used to playing with width all the time and I think that was a problem for us.
"It wasn't working at all," he added.
"We had some possession of the ball but we never really threatened. We had two or three shots from the edge of the box.
"It was a nothing first half, really, and the goal, if anything, made us play.
"(Southampton) scoring the goal right on half-time motivated us a bit to do better."