Josh Brierley had given the West Lancashire League Division One side the lead on 20 minutes with Kevin Edgar doubling the advantage 14 minutes into the second-half.
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Sub Luke McNaughton pulled a goal back on 72 minutes to set up a grandstand finish.
But despite hitting the post in injury time, Hesketh Bank claimed the cup in front of around 400 spectators.
After a cagey start, Josh Brierley swivelled to put Hesketh Bank ahead after the ball fell kindly to him 10 yards out.
Player manager Dan Birkby came close to making it two, a volley going narrowly wide of the left hand post as Wrens struggled to get a foothold in the game.
Jacob Aspinall had Wrens’ best chance when he burst clear only to fire a 20-yarder comfortably over the bar.
The second-half started at a frantic pace, Kevin Edgar’s daisycutter smartly turned round the post by Wrens’ keeper Ethan Smyth.
From the resultant corner sub Ashley Disley stabbed the ball on to the bar before it was cleared to safety.
But Bank didn’t have to wait too long to score their second.
Dan Birkby, played onside by Tarren Moxon, burst into the box and fired goalwards with Smyth saving again.
But Edgar was on hand to stab home from an acute angle to spark wild celebrations in the Hesketh Bank camp.
Craig Doble immediately made a double substitution and one of those subs, Luke McNaughton, halved the deficit firing home from 12 yards on 72 minutes.
As the clock ticked down, Ollie Burgess thought he had grabbed a dramatic equaliser when his 20 yard piledriver took a wicked deflection.
But Hesketh Bank keeper Tom Corbett stuck out a leg to make an incredible instinctive save.
Robbie Hulme then crashed a snapshot against the base of the post in injury time as Wrens piled on the pressure.
Referee Lewis Atkinson, who had an excellent game, then blew his whistle to signal full time and Hesketh Bank’s first ever LFA Amateur Shield win.
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