Hernandez is already a Red Devils cult hero but his two goals on Tuesday night opened the door to European success in his debut season at Old Trafford.
The summer signing scored in each half, propelling the club into the quarter-finals of the Champions League for a fifth successive season.
An own goal by Wes Brown in the 82nd minute ensured a nervous finish but United were not breached again by Marseille and secured their passage.
The only downside for manager Sir Alex Ferguson was that both John O'Shea and his replacement Rafael went off with suspected hamstring injuries.
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.
A minute earlier, however, they had shown their intentions when Wayne Rooney played the ball out to Ryan Giggs but his cross was blocked by Souleymane Diawara.
United took the lead with a sweeping move, Giggs finding 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, who came into the match on the back of five wins in six league games, responded in the ninth minute.
Andre-Pierre Gignac found himself in the clear, only to hook the ball high and wide from a good position.
United had the momentum, though, with Giggs finding plenty of space on the left. The Welsh veteran delivered a cross into the box in the 19th minute but goalkeeper Steve Mandanda made the interception.
Hernandez was then booked two minutes later for a challenge on former Old Trafford favourite Gabriel Heinze before testing Mandanda in the 23rd minute with a header after being released by Rooney.
United maintained the momentum and O'Shea picked out Nani but he dragged his effort wide of the post.
They poured forward again in the 35th minute following a break by O'Shea. However he sent his cross behind Hernandez before limping off.
Marseille should have equalised when 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.
Hernandez then had a claim for a penalty waved away after he went to ground under pressure from Taiwo before Loic Remy went close for Marseille.
United were looking to build on their lead at the start of the second half and Rooney slipped the ball through to Hernandez in the 54th minute but he had strayed offside.
Rooney was beginning to see more of the ball and tried to release Hernandez three minutes later when it had seemed he would go for goal. It proved to be the wrong option as his pass was cut out.
Back came Marseille and Remy skipped to the byline but failed to pick out anyone with his cross.
Ferguson made a switch in the 61st minute, bringing on Antonio Valencia for Nani who had failed to make an impact after a quick recovery from a gashed leg.
Valencia had only returned to action in the victory against Arsenal on Saturday after being out since September with a broken ankle.
United were finding it hard to carve out any openings after a bright start and Marseille were coming more into the game as it entered a crucial phase.
The home side made another enforced change with Rafael also appearing to suffer a hamstring injury. He was replaced by Fabio.
Hernandez extended 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.
Valencia started the move by releasing Giggs 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 Heinze.
That set up a nerve-shredding final few minutes but United held firm to reach the last eight.