The Merseysiders came to the Shay essentially to contain, playing five across the middle and just one up front.
And it worked up to a point, but once Junior Brown had broken the deadlock in the 58th minute there was only ever going to be one winner.
Cavell Coo pressed home Town's advantage four minutes later with a second header and there was a late strike for Ashley Stott from the bench.
Manager Jim Vince was forced to hand a debut to Craig Ellison when Phil Senior - the intended replacement for food poisoning victim Jon Kennedy - witdrew but the keeper was largely untroubled.
And the visitors were a real disappointment as an attacking force for a side that clearly has hopes of repeating last season's third-placed finish.
Jonathan Smith created an early opening for Brown who sent his right foot shot from the edge of the area wide of the United goal.
But Skelmersdale were keen to prove they would be no pushovers and Danny Meadowcroft was forced to defend well on a couple of occasions under pressure from George Donnelly, who also fired wide from a Sean McConville cross.
Town ought to have opened the scoring after 15 minutes when Scott Phelan's crossfield pass picked out Coo.
He crossed for Paul Gedman whose downward header struck United keeper Ryan McMahon on the chest before the ball was cleared.
And moments later Damien Allen fired in an effort from 25 yards that flew into the keeper's arms.
Lincoln Adams did well to block Adam Wade's 18th-minute shot 12 yards from the Town goal and Donnelly was denied again soon after.
But Halifax finished the first half strongly, creating a number of openings without being able to take them.
Allen's 26th-minute corner was headed back across goal by Gedman and punched, unconvincingly, by McMahon to Smith who could only head it back into the keeper's arms.
Colin Daniel got away down the left just before the half hour and crossed for Gedman who nodded the ball back to Allen, but his low shot went wide.
Nigel Jemson struck a shot from a short free kick into the keeper's arms, Brown sent an effort over the top and Gedman managed to snatch a volley over the bar from inside the six yard box after good work by Daniel on the right.
It was all Town, but Daniel fired over four minutes before the break and glanced a header from Coo's long ball forward into the keeper's arms.
Town opened the second half with another Brown chance, created by Jemson's long pass to Gedman, but again the ball went wide.
And Donnelly, who played the lone striker role well, might have done better at the other end after getting round the outside of Jemson.
Moments later Craig Ellison was forced to make his only real save of the afternoon, turning a McConville effort round the post.
But Town eventually broke the deadlock 13 minutes after the break after Allen had picked out Daniel on the left.
He got away from the Skelmersdale defender and stood up his cross for Brown to head home.
Four minutes later Phelan had an effort blocked but the ball bounced back to Allen. He sent a diagonal cross in from the left and Coo dived to head home.
Donnelly flashed a left foot shot across the face of goal and wide on an increasingly rare United attack.
And Peter Moore might have bagged a third Town goal in the 70th but, after playing a one-two with Allen, smashed a shot into the side netting.
Stott let a shot fly from 25 yards that was easily claimed by McMahon and the keeper did well to take the ball off Danny Ellis as he tried to get on the end of another Daniel cross.
McConville missed an absolute sitter in the second of five minutes of injury time, failing to hit the target after good work by Paul McNulty.
And Town made them pay by bagging a third in the dying seconds when Stott got clear, rounded the keeper and had time to compose himself before firing home.

MATCH FACTS
FC Halifax Town: Ellison, Coo, Brown (Ellis), Jemson, Adams, Meadowcroft, J Smith, Allen, Phelan (Moore 69), Gedman (Stott 65), Daniel. Subs (not used): Hinsley, Walker.
Booked: None
Sent-off: None
Goals: Brown 58, Coo 62, Stott 90

Skelmersdale Utd: McMahon, Duffy, Brockley (Houghton 69), Foster, White, Turner, McConville, Birchall, Wade (Kelly 85), Donnelly (McNally 86), Walker. Subs (not used): Pringle, Glaysher.
Booked: Wade (foul 42)
Sent-off: None
Goals: None

Attendance: 1,107
Referee: M J Denton.

STAR SHAYMAN
Damian Allen was making his Shay debut against Skelmersdale, but looked like he had been striding round the pitch for all of his career.
He and Scott Phelan look as though they will make a good central midfield partnership and the former Morecambe man was highly influential.
His pass released Colin Daniel for the opening goal and it was his cross that enabled Cavell Coo to head home the second and effectively wrap up the points.
Daniel had another good game himself and it was only his third appearance for the team.
Once he switched to a position wide on the left he caused untold damage, including providing the cross for Junior Brown's opening goal.
He is a strong player who is happy to take the knocks and can pick a pass when required.
Brown began the fightback at Garforth in midweek and was the catalyst for Town again, in terms of goals, against Skelmersdale.
But even before he struck, a buzz went round the ground whenever he was in possession.
Allen picks up the three points on offer in our season-long competition with Daniel claiming two and Brown one.

PLAYER POINTS
Jonathan Smith 13, Peter Moore 10, Junior Brown 9, Paul Gedman 8, Scott Phelan 5, Ashley Stott 5, Adam Morning 4, Jon Kennedy 4, Steve Payne 3, Lincoln Adams 3, Cavell Coo 3, Colin Daniel 3, Allen Daniel 3, Nigel Jemson 2, Craig Smith 2, Justin Walker 2, Damian Allen 2, Phil Senior 1, Luke Hinsley 1 .

YOU SAY
That was the best all-round performance of the season - 90 minutes of pleasure. Jemson worked hard for his pies - a joy to watch - town fan
90 mins of domination. The fans, players and managment kicked every ball. Get through those ancient turnstiles and have a look. Nice one - Anon

thankyou - skircoat lad