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Substitute Yemi Odubade scored an 89th-minute winner as Maidstone won a home league game for the first time since August.
Odubade had only been on the pitch four minutes when he buried Jamar Loza’s cross in front of the Town End.
Earlier, Liam Enver-Marum cancelled out Macclesfield’s opener, then the visitors missed a penalty before dominating much of the second half - but it was Maidstone’s day at the death.
United, unchanged from the midweek draw at Sutton, were slow to get going against a talented but big Macclesfield side who weren’t afraid to go direct when they needed to.
The hosts looked uncomfortable at the back early on and were behind in the eighth minute to another poor goal, the theme in recent weeks.
This time it came from a hopeful long ball with Jack Sampson given a free flick-on to Chris Holroyd who finished neatly past Lee Worgan.
Holroyd had another glorious chance seconds later, Worgan saving well with his legs.
Seth Twumasi was looking good at right-back as Maidstone started to get a foothold.
The equaliser came on 16 minutes with Loza doing well out wide and reaching the byline before squaring for Enver-Marum to finish.
Enver-Marum’s goal lifted Maidstone and they were almost in front a couple of minutes later, Bobby-Joe Taylor’s fierce hit pushed over by Craig Ross after Twumasi and Loza linked nicely in midfield.
Macclesfield had the chance to go back in front on the half-hour after Tom Mills conceded a debatable penalty, the Stones full-back appearing to get a toe on the ball as he challenged Jack Mackreth.
Referee Carl Brook pointed to the spot but Whitaker’s poor penalty was easily saved by Worgan, diving low to left.
Enver-Marum and Loza were looking increasingly dangerous as a partnership and the pair combined again 10 minutes before half-time, Loza’s outrageous volley from a cross going wide.
Dan Sweeney’s header drifted wide for Stones while Whitaker missed the target when well-placed at the other end.
Macclesfield had a good spell at the start of the second half, seeing plenty of the ball and forcing United back.
Taylor got in the way of Mackreth’s strike after the ball sat up on the edge of the box, then Worgan somehow got his foot to Paul Lewis’ effort from inside the box.
There was respite for Maidstone when Worgan’s quick throw triggered a breakaway involving Taylor, Loza, Ben Greenhalgh and Twumasi.
United didn’t get a shot away but at least showed they could get at a Macclesfield side who’d been well on top after the break.
The Silkmen went close again inside the last 20 minutes, a cracking 30-yard drive from David Fitzpatrick hitting the post, possibly with a touch from Worgan.
The introduction of Jack Paxman helped Maidstone get on the ball and they looked more positive.
There was a minute left when Maidstone pinched the winner, Loza doing well out wide and playing in a dream ball across the six-yard box for substitute Odubade to finish.
Maidstone: Worgan, Twumasi, Mills, Acheampong, Lokko, Rogers, Murphy (Greenhalgh 46mins), Sweeney (Paxman 74mins), Lozar, Enver-Marum (Odubade 85mins), Taylor. Subs not used: Coyle, Evans.
Attendance: 2,114.