In a match of few chances, played out in persistent rain, Brakes deservedly led at half-time courtesy of Courtney Baker-Richardson’s 21st-minute strike.
However, the home side increased their tempo after the break as Leamington struggled to hang on to possession.
Stefan Brown pulled the hosts level in the 63rd minute and there was an air of inevitability about the winner, if not the goalscorer, with centre-back Mike Jones heading home the decider in the 84th.
Brakes kicked off, buoyed by a 500-strong following, but it was Hungerford who were first to threaten, Tony Breeden racing out bravely to claim the ball at the feet of Garyn Preen.
In a cagey first 15 minutes Daniel Dubidat tried his luck with an acrobatic effort for Brakes after Jack Edwards had won a flick-on but the flag was already up for offside while James Clark got his shot all wrong after the visitors had failed to deal with an Ian Herring long throw.
A superb touch from Baker-Richardson, rewarded for his equaliser at Redditch with a starting berth, released Lee Moore on the half-way line and as the midfielder raced into the box, home keeper Paul Strudley slid out to deflect the ball out for a corner.
Preen was booked for a tug back in the build up and when the corner was eventually delivered, Baker-Richardson arrived at the near post to guide Sam Austin’s low cross into the net despite Strudley getting a hand to the ball.
The Crusaders could possibly count themselves a little unfortunate to be trailing after what had gone before but with Jamie Hood a tower of strength at the back for Brakes, there was little sign of an immediate response from the hosts.
Indeed, it was Brakes who were looking the most likeliest to add to their tally with the lively Baker-Richardson combining well with Dubidat down the right to set up a shooting chance for Austin. However, a deflection took the pace of his shot and made it easy for Strudley.
Good pressing from Brakes then stole possession in a promising position but Dubidat was unable to get any power on his shot.
The only defensive concerns for the visitors were coming from Breeden’s erratic kicking and his slip presented Nat Jarvis with a clear run to goal in the 40th minute. However, the striker slid his shot inches past the far post.
The rain went up a notch to torrential during the half-time interval, easing somewhat when the teams re-emerged, with Brakes knowing a clean sheet would guarantee them trips to Halifax, Stockport and Kidderminster next season.
But, with the promised land within their grasp, the visitors went into their shells.
Clark’s shooting skills were again found wanting after he and Brown had caused panic in the Leamington box and he was then unable to direct a header on target after nipping in front of Breeden from a quickly taken throw-in.
Edwards’ header from a Taundry free-kick bounced up into the arms of Strudley but it was a rare sight of goal for Brakes as Hungerford snapped up all the second balls.
The home side were deservedly back on terms in the 63rd minute when Brakes failed to clear their lines and Brown produced a smart finish to find the bottom corner past the advancing Breeden.
Scott Rees was forced off for Hungerford with a back injury in the 68th minute and Dubidat gingerly left the pitch two minutes later with the same complaint.
Halsall was the Leamington man’s replacement, with Baker-Richardson forced to plough a lone furrow up front as the visitors found themselves dropping deeper and deeper.
Nevertheless, the attacker created his next chance himself, blocking an attempted clearance and then firing in a shot which was just wide of the angle.
Brown’s glancing header was collected by Breeden before Clark thought better of shooting from a central position, laying it off to Preen. His measured strike was deflected away for a corner by Taundry and it was from the dead ball that Hungerford scored their winner, Jones ghosting in at the near post to power a header past Breeden.
The defender’s surprise at scoring saw him glancing back at the referee three times before he could start his celebrations in earnest in front of the main stand.
There were still six minutes of normal time and a generous five minutes of injury time for Brakes to find a way back but the belief they had shown when trailing at Redditch was markedly absent.
James Mace powered in a header from a corner which found its way through to Strudley while Ben Mackey was thrown on in the 89th minute in place of Moore.
Breeden tried to inject some urgency with a run which took him deep into Hungerford territory. However, his ball was cut out and only a poor touch from Town substitute Harry Goodger spared the keeper’s blushes with the Leamington captain stranded on the half-way line.
Goodger had another chance to seal the tie as Brakes were again left short-handed at the back but instead of heading for goal, he took the ball into the corner to run down the clock and administer the last rites to Brakes’ promotion challenge.
Hungerford: Paul Strudley, Gary Horgan, Rhys Tyler, Mike Jones, Matt Day, Scott Rees (James Rusby, 68), James Clark, Ian Herring, Nat Jarvis, Stefan Brown, Garyn Preen (Harry Goodger, 89). Subs not used: Mark Draycott, Diak John, Jon Boardman.
Brakes: Tony Breeden, Richard Taundry, Connor Gudger, Jack Edwards, Jamie Hood, James Mace, Lee Moore (Ben Mackey, 89), Callum Gittings, Courtney Baker-Richardson, Daniel Dubidat (Joe Halsall, 70), Sam Austin. Subs not used: Ben George, Rob Ogleby, Rob Elvins.