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Maidstone suffered their second home defeat in just over a week on a frustrating night at the Gallagher Stadium.
Dave Martin's goal in first-half stoppage-time won it for Whitehawk, who climbed into the Vanarama National South play-off places as a result.
Stones remain second, seven points behind leaders Ebbsfleet, although they've now played a game more than their county rivals.
Callum Driver returned from suspension to replace Alex Brown at right-back in Maidstone's only change from the 2-1 win over Truro on Saturday.
This was a second game in three days for Whitehawk, who scored late to earn a 1-1 draw at Dagenham & Redbridge in the FA Cup second round on Sunday and now face a replay for the right to play Everton at Goodison Park.
Former Ebbsfleet skipper Paul Lorraine was missing through injury and there was no Sergio Torres for the visitors while Scott Neilson dropped to the bench in another of manager Steve King's five changes.
Lee Worgan's terrific long kick travelled all the way into the Hawks box and into the path of Alex Flisher but his shot flashed wide - and the flag was up for offside anyway.
However, it was Whitehawk who saw more of the ball in the early stages.
Captain Sam Deering dragged a low shot wide and then had a second effort blocked after the visitors had worked the ball cleverly on the edge of the Stones penalty area.
Martin offered Whitehawk a decent outlet down their left-hand side and when the ex-Dartford man beat a man and crossed for Jake Robinson, Maidstone had to be alert to charge down the striker's shot.
The visitors then thought they'd taken the lead when Robinson smashed a shot past Worgan but their celebrations were cut short by the assistant's flag.
Maidstone had to wait until the 23rd minute for their first chance. Matt Bodkin's cross from the left reached Manny Parry on the six-yard line but the defender's glancing header dropped wide of the far post.
The visitors continued to carry the greater attacking threat and Robinson's low shot across the face of goal deflected behind after Deering had picked him out with a neat pass into feet.
David Ijaha shot wide from distance as Hawks kept pressing but then came a real chance for Maidstone.
Persistence from Frannie Collin down the Stones left earned him a yard of space and his smart cutback picked out Joe Healy, arriving late into the box. Healy hit the ball first time and then probably wished he hadn't as his shot sailed out of the ground.
Maidstone got bodies in the way to block Danny Mills' header from a Martin corner and Robinson lobbed Worgan as the first half entered stoppage time but again the offside flag went up.
But there was no denying Whitehawk the opener with just seconds left before the break. When the ball dropped for Martin near the penalty spot, he turned sharply and rattled a precise shot into the top corner, giving Worgan no chance.
King's side started the second half as they had finished the first, on the attack.
Robinson cut in from the left and shot straight at Worgan, who grabbed a Mills header moments later.
Stones boss Jay Saunders had seen enough and made a double change shortly before the hour mark, sending on Alex Akrofi and James Rogers for Collin and Bodkin.
Akrofi might have made an instant impact when Healy fired the ball across goal from the right but the striker was denied by a crucial last-ditch challenge.
But the visitors looked comfortable and Deering forced another save from Worgan when he was afforded the space in midfield to wind up for an ambitious long-range strike.
Whitehawk keeper Craig Ross was finally called into action on 72 minutes when Alex Brown, Maidstone's final substitute, took aim from 35 yards. Ross dived to his right to save and that brought the home crowd to life.
But still the hosts couldn't build any real attacking pressure and it was Whitehawk who had the next chance, Robinson hooking a volley across goal and just wide.
Whitehawk used every trick in the book to wind the clock down and when Akrofi was presented with a shooting chance inside their box, he scuffed his effort and the visitors cleared their lines.
Substitute Neilson dragged a shot wide and the men in red held on, surviving a scare when Alex Flisher's low shot in the sixth added minute struck the base of the far post.
Maidstone: Worgan, Driver, Mills, Coyle, Parry, Paxman (Brown 65mins), Bodkin (Rogers 56mins), Healy, May, Collin (Akrofi 56mins), Flisher. Subs not used: Birchall, Taylor.
Whitehawk: Ross, Sessegnon, Braham-Barrett, Ijaha (Neilson 77mins), Rose, Gotta, Deering, Mendy, Robinson, Mills, Martin. Subs not used: Stevens, Arnold, Hawkins.
Attendance: 1,743.