A goal from Paul Stoneman on his first start for two years was not enough to save 10-man Halifax from defeat during an incident packed match.
Defender Stoneman steered in a left footed shot through the legs of Morecambe keeper Adam Sollitt from Adam Quinn's lay off on 28 minutes.
Stoneman has been out for the last two years with cruciate ligament injuries to both knees but has made a couple of appearances from the bench in recent weeks.
By the time Stoneman scored, Halifax were 2-0 down thanks to Danny Carlton's strike on 12 minutes and Jim Bentley's diving header on 24 minutes.
But just when a Halifax comeback looked on, Quinn was sent off for a professional foul on 40 minutes.
Defender Quinn was given his marching orders for pulling down Garry Thompson on the edge of the area, even though he was not the last man.
Halifax defender Matt Doughty was covering but Blackburn-based referee Mo Matadar deemed Quinn had to go and he will now miss Saturday's trip to Dagenham & Redbridge.
After the break, Morecombe should have extended their lead but were thwarted by Ian Dunbavin who made four terrific saves to twice deny Wayne Curtis and keep out efforts from Michael Twiss and Kieron Walmsley.
But victory was finally confirmed when Twiss blasted into the top corner from close range on 79 minutes, following substitute Garry Hunter's clever turn and cross.
With a performance of similar calibre next Tuesday, Morecombe could cause Huddersfield some problems and might even produce upset in their LDV Vans trophy first round encounter.