Southampton looked good in the opening exchanges of this game and were rewarded with a half time lead, Richard Chaplow smashing Saints ahead.
But Fergie had a trick or two up his sleeve and with Nani and Ryan Giggs on the field, they looked a different team in the second half
First Michael Owen levelled with his first goal since September, and then Javier Hernandez ghosted in un-noticed to score the goal that would put United trough to the last 16.
After the game, Ferguson told MUTV: "Sometimes we make it difficult for ourselves but, in fairness, I maybe meddled with the system somewhat this afternoon.
"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."