Kosta Barbarouses and Tim Payne scored first-half goals before Oskar Zawada's late penalty pushed Giancarlo Italiano's side to a club-record points haul and highest-ever finish.
They sit on top of the table by a point - for now.
A Central Coast defeat to Newcastle on Saturday would have earned Wellington a first trophy in club history but the Mariners' Â 3-1 win means they can overtake the Kiwi side in a rescheduled match on Wednesday.
Wellington boast 53 points, with the Mariners on 52 ahead of Adelaide United's trip to Gosford. A point will be enough for Central Coast to be premiers.
For the 15,428 Kiwi fans who arrived at the Caketin with high hopes, their victory was bittersweet.
In their 17 years, Wellington have not been within touching distance of a trophy, with the Premiers Plate flown over the Tasman and stowed away under the stadium in case their time had come.
Plans for the trophy to be on display or in the chairman's lounge were scotched when coach Giancarlo Italiano declared he didn't want himself or his team to see it, calling it "kryptonite".
Wellington produced a first-half worthy of title-winners, bossing the finals-bound Macarthur side.
The Nix pushed and probed around the box, before going route one: a long-ball delivering a 21th-minute opener.
Nicholas Pennington produced a superb pass from the deep to play Barbarouses through, the forward taking a touch and burying a record-breaking goal.
Barbarouses' 13th strike of the campaign was his 93rd A-League goal, placing him fourth in the all-time league list, and the top-scoring Kiwi after overtaking Shane Smeltz.
Just before the half-hour mark, Payne doubled the lead with a powerful back-post header from Ben Old's chipped cross.
Like Barbarouses, Old was enjoying far too much space, and might have scored himself, shooting a good chance straight at Filip Kurto and hitting the bar from a cross earlier in the half.
Old's trickery produced the third, dribbling into the box and laying off to Zawada, who went down under a rash challenge and converted an injury-time penalty.
Macarthur - who were playing for third place - enjoyed a decent spell at the top of the second half but were otherwise lamentable as they slipped to a third defeat of the season to Wellington.
Mile Sterjovski's side will now finish fourth, or fifth if Sydney FC defeat Perth Glory on Sunday.