United go seven points clear as Chelsea stumble
Southampton took a shock third minute lead when Michael Carrick's poor back-pass left David de Gea in trouble, with Jay Rodriguez dispossessing the goalkeeper before rolling the ball into the net.
However, United were only behind for five minutes with Rooney equalising after the England striker was played in by Shinji Kagawa.
And Rooney made it 2-1 in the 27th minute after a Robin van Persie free-kick was headed back across goal by Patrice Evra.
United had the ball in the Saints net for a third time but the 'goal' was disallowed for offside.
The Blues, held to a draw by third-tier Brentford in the FA Cup, had to wait until first-half stoppage-time before taking the lead at the Madejski Stadium, with a neat pass from Fernando Torres setting up his fellow Spaniard Juan Mata, who drilled a low shot into the net.
Frank Lampard, repeatedly linked with a move away from Chelsea despite impressing yet again this term, made it 2-0 in the 66th minute when he rose above the Royals' defence to head in a corner.
But Le Fondre increased the pressure on Chelsea interim manager Rafael Benitez with two well-struck goals in the final three minutes.
Liverpool needed just five minutes to take the lead at the Emirates after a series of mistakes involving Bacary Sagna, Thomas Vermaelen and Aaron Ramsey created a chance for Daniel Sturridge, whose shot was saved.
More bad Arsenal defending allowed Jordan Henderson to burst into the penalty area before his initial shot was blocked only for the midfielder to score on the follow-up in the 60th minute.
But within a few minutes Arsenal scored twice.
Olivier Giroud headed in Jack Wilshere's free-kick and the Frenchman then turned provider for Theo Walcott, who equalised with a powerful shot.
Tottenham remained fourth thanks to Gareth Bale's superb leveller in a 1-1 draw away to Norwich.
The Canaries, fresh from the embarrassment of being knocked out of the FA Cup by non-league Luton, went ahead when Wes Hoolahan turned in Anthony Pilkington's 32nd minute cross.
But Wales winger Bale struck in the 80th minute when he collected the ball inside his own half, ran at the defence and curled a shot across the goalkeeper.
Fifth-placed Everton closed to within a point of Tottenham after a 2-1 win at home to West Bromwich Albion.
Baines then doubled Everton's lead with a penalty on the stroke of half-time after Claudio Yacob brought down Victor Anichebe in the box.
Shane Long pulled a goal back for the Baggies with a 65th minute header.
Meanwhile Fulham beat London rivals West Ham 3-1 at Craven Cottage.
Bulgaria striker Dimitar Berbatov celebrated his 32nd birthday by opening the scoring for Fulham with a 10th minute header.
Joey O'Brien's late own-goal sealed Fulham's victory.
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