James Armson scored a controversial injury time penalty rebound to send unbeaten Nuneaton Town third in Skrill Premier.
Boro fell behind after four minutes to a fine strike from Anthony Malbon.
They struggled early on but gradually grew into the game and levelled after 82 minutes through Louis Moult’s fourth of the season.
Just when it looked like being a fair draw, Nuneaton were given a 92nd minute penalty when former Boro man Kyle Storer was adjudged to have handled.
It was a harsh decision but it initially looked like justice had been done as Danny Lewis saved Armson’s poor penalty.
However, the ball ricocheted off Mickey Demetriou straight to Armson and he turned it in to the open goal to spark mass celebrations.
Manager Kevin Wilkin said: “I guess over 90 minutes it was fairly even. We had a lot of the second half.
“A draw would probably have been fair. We worked so hard though.
“I don’t think anyone can begrudge us a bit of luck.
“I didn’t really see if it was a penalty. You can’t lift your arms up though.”
There was one change to the team which drew 1-1 with Barnet on Saturday as James Belshaw returned in goal for Dimitar Evtimov.
Wilkin continued his policy of giving both a chance to stake their claim to be No.1 in the long term.
The only other change in the squad saw Mark Bell make his first appearance. He was on the bench in place of David McNamee.
It is believed he had trouble getting to the game in time to be selected.
Harriers included the son of former Boro legend Terry Angus in their team as Dior Angus started on the right wing.
Dior almost signed for Boro in the summer before Harriers nipped in.
Ex-Nuneaton midfielder Storer skippered the team and James Dance, who had a loan spell with Boro last season, was on the bench.
Nuneaton were behind after just four minutes through a moment of real quality from Malbon.
Michael Gash bundled through a robust challenge from Dean and the ball broke for Malbon on the corner of the box.
There was no hesitation from him as he curled a brilliant shot over Belshaw and into the far corner of the net.
Harriers were in the ascendancy early on as they moved the ball impressively.
Jack Byrne fired a 20 yard shot straight at Belshaw before the keeper made a good save from Angus after he combined with Gash.
The hosts almost conjured an unlikely equaliser after 23 minutes when Armson’s floated free-kick was met at the back post by Gavin Cowan with a fine header.
Moult and Theo Streete threw themselves at it but Storer connected and he cleared off the line.
The rebound fell for Gaz Dean but he missed his kick when he should have done much better.
Three minutes later Nuneaton went close again as they looked dangerous from dead balls.
This time Armson drilled a corner in and Andy Brown’s header was cleared off the line by Lee Vaughan.
Nuneaton almost fell two behind a minute after the restart.
Belshaw could only punch to the edge of the box.
Gash scuffed his shot from 16 yards but it would have gone in if Amari’i Bell had not cleared off the line.
The danger was not gone and Dean was called on to make another excellent block.
Boro’s first chance of the second half came after 58 minutes when Amari’i Bell and Danny Sleath combined to cross for Brown, who headed a yard over.
Jack Byrne burst through after 63 minutes but he fired wide under heavy pressure from Dean.
Nuneaton were getting into good areas but were unable to find the final killer ball.
Although Moult fired over from distance a change was needed and it came after 71 minutes when Greg Pearson replaced Wes York.
Kidderminster remained a big threat to get the second, Chey Dunkley forcing a sharp save from Belshaw with 15 minutes to go.
Sleath’s final act of the game was to fire wide from 20 yards as Mark Bell came on for his debut. Boro stayed 4-4-2 but Moult shifted to the right wing.
It worked perfectly as Moult levelled after 83 minutes.
He drifted into the centre to receive the ball 20 yards out, turned and fired into the bottom right corner.
It looked set to finish 1-1 but in injury time Boro won it.
Harriers had given away a plethora of free-kicks but the most important came at the death. Mark Bell fired in a powerful shot that struck Storer on the upper arm.
No one appealed but the referee pointed to the spot for a harsh spot kick.
Armson looked to have blown it when his poorly hit penalty was saved.
The rebound hit Demetriou and was bundled over the line by Armson despite Pearson being credited with the goal.