Stanley, who started the afternoon a point behind the Town, scored with virtually the last kick of each half after Sean McConville put them in front a minute before half-time, then the division’s top scorer, Billy Kee, bagged a 93rd-minute goal to nick the victory.
The Hatters had been the better side overall but spurned several good opportunities, both before and after Elliot Lee had hauled them level with his tenth goal of the season just after the hour.
Ultimately it was Stanley, however, who brought the Town’s five-match unbeaten run to an agonising halt, and extended their own sequence without defeat to eight matches, seven of them victories that see them move two points above the Town.
Jones made two changes from last week’s draw at Cambridge, with midfielder Andrew Shinnie and Elliot Lee, making his first start since suffering a shoulder injury against Wycombe at the end of January, coming back into the team in place of the injured Lawson D’Ath and James Collins, who was serving his one match ban after being sent off at the Abbey.
The Hatters came racing out of the blocks and within the opening minute Danny Hylton almost got in on the end of a long clearance by Marek Stech, then Dan Potts rose highest to meet the resulting corner from Alan Sheehan, but his towering header was cleared off the line.
The same combination provided the next opening a couple of minutes later, Sheehan picking out Potts with a free-kick, and although the left-back didn’t connect cleanly with his header, there were claims for a penalty for handball as referee Darren Drysdale pointed for another corner.
The Hatters were playing some cracking stuff, while the back four stood strong to a series of crosses
Elliot Lee was looking lively and just after the quarter-of-an-hour mark the forward took a ball from Berry to the byline and tricked his way past Mark Hughes, only to be denied with his poke towards the near post by a deflection from a sliding challenge by skipper Seamus Conneely.
The ex-Barnsley man was next to have a go too, picking the ball up 25 yards out and firing right-footed at goal, but Stanley keeper Aaron Chapman saved well diving low to his right.
Stech was called into action in the 20th minute when Jordan Clark’s speculative effort deflected high into the air off Glen Rea’s head and the Czech keeper had to race back to his line to paw the ball over the bar.
Then, with 26 minutes on the clock, Sean McConville’s 15-yard shot from Kayden Jackson’s knock-down went safely over as Accrington started to have a go.
The Town had been the better side though, and after a spell of possession on the half-hour, working the ball in both halves as they probed for an opening, the lead almost came when Hylton took Sheehan’s long pass on his chest and Shinnie arced in a cross from the right that just eluded Elliot Lee’s outstretched boot, and Berry racing in behind him.
More patient passing around the edge of the area brought another chance on 32 minutes, this time for Shinnie, who took Hylton’s short ball and tried to bend one around Chapman from 20 yards, but it flashed just past the wrong side of the post.
In the 38th minute, Hylton received a ball from Berry and hit a rasping drive that Chapman did well to turn behind, then Potts rose to meet Sheehan’s left-wing corner in an exact repeat of his first chance in the opening minute, only for Jimmy Dunne to clear off the line for a second time.
Town had played well to that point, but were made to pay for not converting their chances when McConville bent a terrific effort into the top corner from 25 yards a minute before half-time.
Accrington finished the half strongly, Billy Kee firing straight at Stech – and then they started the second well too, Jackson creating space for himself 25 yards out, but again the Town keeper was equal to his tame effort.
The Hatters had a great chance to mount a counter attack in the 52nd minute when Hylton and Shinnie combined to set Berry free inside his own half.
The midfielder burst forward only to be tripped by Hughes, with Drysdale quick to blow his whistle – then show the Stanley defender a yellow card – without waiting to see the ball had reached Hylton on the verge of the visitors’ box.
The Town kept pouring forward, and Hylton met a Stacey cross with a header that was easy for Chapman, then – in the 56th minute – Flynn Downes spread the ball wide to Elliot Lee on the right, but the striker’s low left footed shot went the wrong side of Chapman’s near post.
Just after the hour his moment came, however, when he was picked out brilliantly by Jack Stacey at the end of a move down the right that started with Stech.
The keeper claimed a cross at the far post, then threw the ball out to Stacey on the touchline and the full-back looked up and bent a fantastic cross-field pass that beat two defenders in the air and found Elliot Lee just inside the area.
The striker bided his time and checked back onto his right foot to fire low past Chapman for the leveller and make it into double figures for the season.
Jones introduced Harry Cornick for Downes in the 63rd minute, and the pacey forward immediately brought another surge to the Town’s attacks as part of a front three, with Olly Lee dropping deeper to anchor the midfield.
Accrington had a chance in the 67th minute when Brown’s shot flashed just past the post, but seconds later Chapman had to tip Cornick’s cross-shot over the bar, then he had to pounce on a loose ball by the post as Potts met the resulting corner with another towering header and Glen Rea attempted to turn it in from close range.
It was all one-way traffic now and in the 74th minute Olly Lee threaded a ball through for Stacey, but Chapman once again produced a fine save as the full-back let fly from inside the box.
A minute later it was Eliott Lee’s turn again, cutting in from the left only for his right-footed curling shot to fly over, then Olly Lee and Shinnie combined to put Stacey in again on the right, and the full-back’s cross found Hylton, but his glancing header went just wide.
The Hatters continued to knock on the door and did everything they could to break down the visitors’ defence, but were hit by the ultimate sucker-punch when Kee picked up a loose ball 25 yards out and shot low past Stech into the bottom corner.
There was an air of disbelief around Kenilworth Road, and the Hatters were off top spot with little time to respond.
But with Cambridge netting a late leveller at Wycombe, the gap to fourth place is still a healthy six points – seven when the Hatters’ goal difference is taken into account – with a chance to improve on that when they head to Coventry on Tuesday night.
TOWN: Stech, Stacey, Rea, Sheehan, Potts, Downes (Cornick 63), O Lee, Berry, Shinnie (Gambin 85), E Lee (Jervis 90+1), Hylton. Subs: Justin, Cuthbert, Mpanzu, Shea (GK)
Goals: E Lee 61
Yellows: E Lee, Sheehan, O Lee, Gambin
STANLEY: Chapman, Dunne, Hughes, Donacien, Clark, Brown, Jackson, McConville, Johnson, Conneely ©, Kee. Subs: Richards-Everton, Nolan, Zanzarlan, Williams, Maxted, De Sousa, Rodgers
Goals: McConville 44, Kee 90+3
Yellows: Hughes, McConville, Donacien, Jackson
REFEREE: Darren Drysdale
ATT: 9,503 (205 away)