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On the half hour mark, Frome had their first effort on goal as the ball was cleared from a corner and broke to defender Dave Thompson, who fired wide from outside the Arlesey box.
After ending the first period on a high, Frome thought they had made a dream start to the second period when Ballinger's free kick was nodded over the line by Rhys Baggridge but the home side's celebrations were cut short by the linesman's flag, with Ricky Hulbert deemed the offender.
Matt Smith whipped in an inch perfect cross from the right flank, which looped on to the head of Perrott arriving at the far post but the Robins man couldn't get his header on target.
The hosts had the majority of the early possession but Arlesey went close to taking the lead on the night with around 15 minutes on the clock from Drew Roberts' free kick.
In the 64th minute, Frome should have found themselves ahead in the tie.
Frome Town 1 Arlesey Town 1 Arlesey Town win 2
But despite the hosts' dominance, the visitors dealt Derek Graham's men a body blow in the final minute of the first half of extra time.
Then, moments before the half time whistle, a misdirected header from Arlesey's Ryan Frater saw Ballinger nip in behind the defence but the angle was too tight for the forward to get away a shot on goal.
But as the game drew to a close, Frome dug deep and came within inches of snatching an equaliser.
With 45 minutes on the clock a smart ball from defence saw the Robins' Dean Nike Air Presto Dark Grey Anthracite
A long ball was cleared up into the air by the Frome defence and Arlesey's Dillon watched the ball drop all the way onto his left foot before swivelling and hitting a stunning strike into the net, that gave a sprawling Chitty no chance.
But the first half action wasn't Nike Presto Leather over.
In the 39th minute, the visitors' Roberts tried for goal again with a set piece strike and this time, his shot looped narrowly over the bar.
Frome roared back at the start of the first half of the added period and Nike Air Presto Winter
The final whistle was looming but a bizarre clash off the ball saw proceedings extended thanks to a lengthy delay.
FROME TOWN: Darren Chitty, Dave Thompson, Rhys Baggridge, Josh Ford, Tom Evans, Mark Cooper (Jed Harper Penman 76), Matt Smith, Dean Evans (c), Luke Ballinger, Mike Perrott, Ricky Hulbert (Mitchell Bryant 90).
With 76 minutes on the clock, the visitors fashioned another chance as Roberts' cross from deep found Dillon in the box but the striker got his diving header all wrong and the opportunity went begging.
Mike Perrott cut inside from the right wing and hit a left footed strike past the near post and shortly afterwards, another Perrot shot took a deflection off Frater but didn't trouble the Arlesey keeper.
The striker smacked an effort goalwards from well outside the area and Robins keeper Darren Chitty first appeared to misread the flight of the ball before reacting sharply to push Roberts' strike on to the crossbar.
Arlesey had been anonymous in the second half but they burst into life minutes later as substitute Christopher Marsh played in Chris Dillon, who was first denied by a strong save from Chitty before his effort on the rebound was blocked on the line by the well placed Thompson.
THERE was no fairytale ending to Frome Town's Red Insure Cup run as an extra time moment of magic from Arlesey Town's Chris Dillon saw them claim the silverware at Badgers Hill.
A limping Ballinger floated in a corner kick and keeper Chitty, who had come forward in a last throw of the dice, connected and headed on towards the goalmouth.
Baggridge found himself on the line and stretched to apply the final touch on the goal line but the Frome fans were left with their heads in their hands as the defender's effort sailed over the crossbar.
The hosts were shell shocked and in the second half of extra time, the visitors' James Air Presto Triple Black On Feet
After requiring a few minutes of medical attention for a broken nose, Eaton was fit to resume his officiating duties but it only delayed the inevitable as Arlesey saw the game out to claim the cup.
Arlesey began to turn the screw in the closing stages but the Robins remained steadfast as the tie went into extra time.
Derek Graham's Robins put in a spirited performance and forced extra time as they led 1 0 after 90 minutes but Arlesey striker Dillon's bolt from the blue sealed a 2 1 aggregate victory for the visitors and saw them take the cup back to Bedfordshire.
when substitute Jed Harper Penman set up Smith, the midfielder unleashed a powerful strike toward the top corner, that was clawed away by keeper Abbey.
Hatch broke away towards goal and looked certain to have a free strike at Chitty's goal but was denied by a last ditch block from Thompson.
The Frome fans were screaming for a penalty in the closing stages of the half when Luke Ballinger was out muscled by Daniel Gordon but referee Derek Eaton was unmoved.
Referee Eaton was caught unawares as Arlesey midfielder Oliver Thorne smacked into the back of him, knocking the official for six as he lay prone on the ground.
Evans steal in behind the visitors' back line and the midfielder held his nerve to fire home across keeper Nathan Abbey and put his side back in the cup final.
In the 101st minute, Frome went close again when Dean Evans laid the ball off to Harper Penman, whose strike from the edge of the area rose narrowly over the crossbar.
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