Manchester United 2 // Marseille 1 (Manchester United win 2-1 on aggregate)
Hernandez scored either side of half-time to make it five goals in five appearances and take his tally to 16 goals in his debut season.
However they had to endure a nerve-shredding final few minutes after an own goal from Wes Brown in the 82nd minute.
Following a goalless draw in the opening leg in France three weeks ago, United, with Hernandez selected ahead of Dimitar Berbatov, got off to a flying start with an opening goal from the Mexican in the fifth minute. Ryan Giggs found Wayne Rooney from the left flank with a short pass. The striker played the ball to the far post with Hernandez tapping it in.
It was just what Ferguson was looking for as it put his side one goal ahead on aggregate. However Marseille nearly responded when Andre-Pierre Gignac found himself in the clear, only to hook the ball high and wide from a good position.
Marseille should have equalised when Souleymane Diawara got on the end of a cross from Taye Taiwo but from six yards out and unmarked he somehow contrived to head wide. It was a scare for United and showed just how finely balanced this tie was despite Hernandez's early goal.
However, the 22-year-old doubled United's lead in the 76th minute with another clinical finish for his fifth goal in five games, taking his tally to 16 for the season.
Giggs started the move by releasing substitute Antonio Valencia and he in turn whipped the ball across to Hernandez, who made no mistake.
But Marseille responded and Brown headed into his own net in the 82nd minute under fierce pressure from former Old Trafford favourite Gabriel Heinze.
That set up a nerve-shredding final few minutes but United held firm to reach the last-eight.