United, under pressure not to concede following a 0-0 draw in the first leg in Marseille, started strongly and were rewarded when Rooney's pinpoint cross found Hernandez who turned the ball into an empty net.
Missing Vidic and Rio ferdinand, United coped comfortably with Marseille's attack and Rooney and Hernandez enjoyed plenty of possession without creating many clear chances.
Andre-Pierre Gignac and Soulemayne Diawara missed good chances to equalise and the French side worked tirelessly after halftime, pinning the home team back but lacking the craft to threaten Edwin van der Sar's goal.
Substitute Antonio Valencia created the second United goal with a deft through pass to Giggs whose neat cross was gleefully swept home by Hernandez.
Marseille refused to lie down and they were rewarded when Brown headed a corner towards his own goal and Paul Scholes was unable to stop the ball crossing the line.
But United kept their shape well in the closing minutes and remained on course for their fourth European Cup and a treble of trophies this season.
Javier Hernandez (right) of Manchester United celebrates with teammate Michael Carrick
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