Rooney opened the scoring when he headed in Patrice Evra's cross on three minutes but James Morrison equalised with a long-range shot.
United survived when referee Chris Foy turned down a penalty claim after Gary Neville sent Graham Dorrans flying when the midfielder was clean through.
Peter Odemwingie later fired a penalty wide after Rio Ferdinand had fouled Jerome Thomas but Hernandez wrapped up the win with 15 minutes to go.
Manchester City are still level on points with their rivals after they won 1-0 at home to Blackpool.
Adam Johnson shot home from long distance after the visitors had only cleared the ball to the edge of their area.
City should have gone further ahead when Luke Varney fouled Yaya Toure but Carlos Tevez put the penalty wide.
Arsenal remain just two points behind the Manchester clubs in third place following an impressive 3-0 win at Birmingham in the late game.
Robin van Persie's deflected free-kick on 13 minutes put the Gunners in charge, and Samir Nasri produced a beauty early in the second half to double their advantage.
A Roger Johnson own goal on 66 minutes wrapped things up as Arsene Wenger's men topped off a dominant performance.
Joe Cole earned under-pressure Liverpool manager Roy Hodgson a vital 2-1 win after they had gone behind at home to Bolton.
Kevin Davies was left unmarked at the back post to head in just before half-time at Anfield.
Matt Taylor had earlier cleared a shot from Maxi Rodriguez off the line and Lucas Leiva pushed the ball wide when left unmarked from a Dirk Kuyt cross in first-half stoppage time.
Liverpool drew level when half-time substitute Steven Gerrard chipped the ball into the path of Fernando Torres who fired in.
Cole netted the winner when Gerrard's deep cross fell to him off a defender in added time.
West Ham moved out of the bottom three with a 2-0 home win over fellow relegation candidates Wolves.
The Hammers went ahead through a Ronald Zubar own goal after 51 minutes. Carlton Cole failed to get a touch on a cross from Frederic Piquionne and the ball hit Zubar and went in.
Freddie Sears netted the second when he shot home after Tal Ben Haim had slid the ball to him with 10 minutes to go.
Tottenham beat Fulham 1-0 as Gareth Bale headed the only goal.
A free-kick from Rafael van der Vaart was headed past Mark Schwarzer by Bale who had been stood in the defensive wall.
Spurs have moved above Chelsea into fourth ahead of the Blues' clash against Aston Villa on Sunday.
Goals from Danny Welbeck, Darren Bent and Asamoah Gyan earned Sunderland a 3-0 win at home to Blackburn.
Welbeck opened the scoring when his shot from the edge of the area was deflected past goalkeeper Mark Bunn by Ryan Nelsen and Bent made it 2-0 when he headed in a cross from Ahmed Elmohamady.
Gyan wrapped up the win just before the end.
Stoke won 2-0 at home to Everton, Kenwyne Jones rising to head in a cross from Matthew Etherington to give them the lead.
Phil Jagielka extended Stoke's lead when he flicked the loose ball in after the visitors had failed to clear when Jones headed on a long free-kick.
West Brom 1-2 Manchester United
West Ham 2-0 Wolves
Stoke 2-0 Everton
Manchester City 1-0 Blackpool
Tottenham Hotspur 1-0 Fulham
Sunderland 3-0 Blackburn Rovers
Liverpool 2-1 Bolton
Birmingham City 0-3 Arsenal