A last minute goal gave a scoreline a more realistic appearance, but it could have been so different had Northwich converted their penalty.
Morecambe started brightly moving the ball round at will but Craig Stanley was unable to get power behind his shot and it was a comfortable save for Phil Senior. Danny Carlton then strayed offside as the Shrimps tried to carry on their good work.
The visitors continued in fine form and pressured the Vics into conceding a foul in a dangerous position. The ball was rolled to Michael Twiss but he sliced his shot wide.
Northwich finally made a showing in the tenth minute. After winning a corner Tony Gallimore swung the ball to the far post from where Michael Carr headed across the face of goal with no-one able to finish off the move.
Shortly afterwards a rampaging run from Gallimore was stopped on the edge of the box, before Northwich were awarded a penalty in the 15th minute. Michael Byrne's cross from the right was to adjudged to have been handled by Chris Blackburn to the outrage of the visitors.
Johnny Allan stepped up but Steve Drench chose the right way and saved low to his left.
The game continued at a pace and Carlton almost nipped in to open the scoring for Morecambe. Senior had difficulty dealing with a pass back and his attempted clearance was charged down, to the home fans' relief the ball was scrambled away.
Morecambe's pressure finally told in the 27th minute when a left-footer out of the blue from Twiss screamed past the keeper.
Carlton missed a chance to double the lead two minutes later when he scuffed wide from a good position. Carr had a difficult chance for Northwich in first-half injury-time but Morecambe were good value for their interval lead.
Morecambe earned two corners in quick succession after the break but Northwich cleared their lines. However the home team almost conceded a second when Adam Yates was given space to attack down the right and put in a telling cross, only for Carlton to mistime his run and the chance went begging.
The visitors continued to call the tune and Stanley was the next to try his luck with an off-target shot and then Gary Thompson just failed to get on the end of a shrewd through ball.
Kevin Townson gave a warning that the game was not yet Morecambe's when he fired in a shot from 25 yards, but Drench was well positioned to make the save.
The keeper then did well to command his area and field a dangerous corner.
At this stage there was more fluency in Northwich's play and Chris Williams was able to get on the end of a flowing move, but his attempted through ball failed to reach its target.
Carlton was hauled down at the edge of the box but the free-kick was overplayed and cleared and then Senior had to race from his area to clear as Carlton was once again played through.
Senior was called into action again shortly afterwards when Thompson cut in from the right, firing in a dipping shot that the keeper was able to parry.
As the game entered its closing stages Paul Brayson did well to find Carlos Roca in a rare attacking move for Northwich, but the cross came to nothing.
Northwich pushed hard in the dying minutes, but pressure was easily soaked up and Twiss settled the match when he was put clear to fire home in the final minute.