The creative midfielder arrowed a strike into the top corner in the 13th minute, leaving Callum Hawkins with no chance in the Brakes net.
Several chances went begging for James Rowe’s side and the visitors threatened too but failed to capitalise in this final match of the regular season.
Rowe, who had started with 10 different outfield players in the previous two games with Fylde's play-off spot secure, again made multiple changes.
There was a welcome return for goalkeeper Chris Neal, while midfielder Will Hatfield was back after a three-match suspension.
Having dropped to the bench for last Monday's defeat at York City, Haughton took the game by the scruff of the neck as he picked up a loose ball 25 yards from goal and let fly into the top corner.
It left the 27-year-old second in the league scoring charts, two behind Macaulay Langstaff of champions Gateshead.
Leamington arrived on the Fylde coast safe from relegation and looking to express themselves going forward, which they did after Haughton’s goal.
Devon Kelly-Evans lifted a free-kick over the bar after Hatfield was penalised for handball on the edge of the area, then Dan Meredith let fly from distance only to be denied by a diving Neal.
Douglas Taylor twice went close to doubling Fylde's lead before the interval.
First Hawkins got across well to hold the striker's acrobatic effort, then Taylor's header from a delicious Hatfield cross cannoned back off the foot of a post.
Two quickfire chances presented themselves to the Coasters in the first 10 minutes of the second half.
Taylor went close again, when Luke Conlan poked the ball through, but his venomous shot was palmed away by Hawkins.
Haughton then clipped a ball in behind the Brakes defence for Sam Osborne, though again Hawkins stood firm to stop the former Leamington player's shot.
It wasn’t all Fylde as Adam Walker seized on a loose ball bouncing around the penalty area but his effort was headed away by Danny Philliskirk.
Taylor had a chance to start and finish another good Fylde move but thumped wide when set up by Ben Tollitt.
Substitute Stephen Dobbie had the final opportunity to put icing on the cake ahead of next Sunday's play-off semi-final but Hawkins denied him with an outstretched leg.
Fylde will host the winners of Thursday's eliminator between Kidderminster Harriers and Boston United, who overhauled Kettering Town for the final play-off spot.
York City earned home advantage against Chorley in Wednesday's play-off opener for the right to visit Brackley Town in the first semi on Saturday.
Fylde: Neal, Morrison, Davis, Whitmore, Walker (Tollitt 58), Conlan, Philliskirk, Hatfield (Whitehead 64), Haughton (Dobbie 77), Osborne, Taylor; Subs not used: Stott, Burke, Whitehead, Dobbie.
Leamington: Hawkins, Meredith, Morley, Clarke (Bushaj 66), Mace, Lane, Williams, Walker, Turner (Olakoko 77), Edwards (Parker 64), Kelly-Evans; Subs not used: English, Taylor.