United brushed aside Wigan, who self-destructed in the second half with two unnecessary red cards, but perhaps more importantly Rooney made his first appearance since the contract saga that saw the England striker threaten to leave before signing a new five-year deal.
The setbacks suffered by Arsenal and Chelsea made it imperative that United did not slip up too and they made no mistake as headers by Patrice Evra and Javier Hernandez ensured Ferguson's men second spot in the Premier League table, behind Chelsea only on goal difference.
Rooney should have put the icing on the cake by scoring too but passed up a glorious opportunity.
For Wigan, red cards for Antolin Alcaraz and Hugo Rodallega virtually ensured they would get nothing from the game.
Roberto Martinez's men had started well, showing from the start however that they were not going to lie down and be rolled over.
The visitors were presented with a fabulous chance in the opening exchanges to stun United when Nemanja Vidic slipped as he tried to clear Charles N'Zogbia's cross. The ball popped up in the air and Jordi Gomez should have at least hit the target - instead he scooped over to the huge relief of most of those inside Old Trafford.
Nani's free-kick from deep on the left nearly surprised Ali Al Habsi in the Wigan goal, but he managed a scrambled save, before Rodallega charged through the United defence and drove in a shot, but it was straight at Edwin van der Sar.
Al Habsi had to be smart to keep out Nani again but Wigan showed their threat on the break when N'Zogbia swept into the penalty area but his shot - with his right foot rather than his favoured left - was disappointing from a good position.
There was another let-off for United when Ronnie Stam stabbed wide after United's defence looked all at sea again, then N'Zogbia burst between Ferdinand and Rafael and was only denied by Van der Sar coming out to block.
From the corner Rodallega tried the spectacular with an overhead kick but the ball went miles wide.
After so many let-offs the stage seemed set for United to make Wigan pay and so it turned out in the last minute of the half as Evra scored his first goal for three and a half years.
Park Ji Sung floated a cross to the back post and Evra rose and sent a downward header past Al Habsi.
Rooney came on in the 57th minute to cheers and some boos as he and Paul Scholes replaced Macheda and Park.
Almost immediately the match swung even further in United's favour as Wigan skipper Alcaraz was sent off after picking up his second yellow card for rash and needless challenge on Darren Fletcher.
Wigan completely lost their heads and two minutes later Rodallega was following his captain down the tunnel after a crazy two-footed challenge on Rafael.
That left Wigan to play for half an hour with just nine men and Ferguson went for the jugular with Hernandez coming on for Michael Carrick.
Rooney, with only a penalty to his name this season, nearly made it 2-0 when he rose above Steve Gohouri and sent a fierce header goalwards only for Al Habsi to tip over.
It did not take long for United to get the goal however as Hernandez's powerful diving header from Rafael's cross easily beat Al Habsi.
Hendry Thomas tried to get Wigan back into it with a long-range free-kick that was easy for Van der Sar before Rooney should have put away the easiest of chances in injury time.
Nani's cross reached Rooney inside the six-yard box but he did not make good contact and Al Habsi was able to save.