The Latics had not even managed a draw in 14 previous meetings with their north-west neighbours, but Shaun Maloney's curling strike four minutes after the break brought that record to an end and allowed Wigan to clamber out of the relegation zone for the first time since October.
"Wigan were the better team," said Ferguson, as his side had an eight-match winning run brought to an end, suffering their first defeat since January in the process.
"They are very under-rated team and we were completely dominated in the first half. We were second to every ball and only had one shot at goal. It was one of these off nights you get.
"We have been on a great run and it has put us in a position where we can win the league, so we have to get over the disappointment of tonight."
Wigan boss Roberto Martinez said: "It has been such a tough week since the Chelsea game.
"But we could not to feel we had someone to blame or be sorry for ourselves. It was very important that we focussed on our performance.
"At half-time it was exactly the same. The players had a real anger about them but we used it to our advantage.
"The players showed a mature side to their approach.
"To perform like we did, against Manchester United, with the record we had against them, speaks volumes about the minds of these players."
Source: PA
Source: PA