Daniel Maddison netted on the half-hour mark for Hebburn, but Jamie Bennett found an equaliser early in the second period.
Nathan Grainger poked home with the last touch of the game, handing Shotton Colliery the Durham County FA Minor Cup in thrilling fashion.
A chilly evening in Seaham began in a fast-paced fashion, with The Yakkas' Bennett hooking the ball over from the edge of the area on six minutes.
With 17 on the clock, Maddison slipped into the area with tricky footwork, but his low attempt could only find the side netting following a last-ditch block.
On 29 minutes, a menacing cross wasn't dealt with by The Hornets, but left-back Tom Goundry could only fire over at the back stick.
A minute later, Gary Henry's side broke the deadlock.
Robbie Gateshill tried his luck with a driven effort from 25-yards, and Mason Beckett could only parry to Maddison for a simple tap-in at the back post.
Hebburn were handed another excellent chance to double the advantage moments later as John Murray was sent in one-on-one, however the number nine's premium opportunity flew off-target.
On the brink of half-time, Luke Hudson's looping free-kick found the head of Murray, but his powerful header whistled over the bar.
After the break, Shotton pegged back on level terms through Bennett.
A deep cross fell perfectly to the feet of the menacing frontman, who calmly poked past Kieran Hunter from close-range.
On 67 minutes, Beckett's loose pass was picked up by David Stansfield, with the substitute's hopeful lob from 20-yards sailing over.
Bennett was played through for a second on the 70 mark, but the attacker struck wide one-on-one.
Reece Kenney tricked his way down the line for The Yakkas on 77 minutes, before dangerously flashing a low ball across the face of goal which luckily evaded the Shotton frontline.
Three minutes from the final whistle, Maddison looked for the bottom corner from outside the area, but Beckett met the shot to keep the score level.
On the 90 mark, Bennett finessed the ball from 20-yards, which just skimmed the far post for Shotton.
Three minutes into injury time, The Yakkas netted the winner.
Substitute Anthony Rookes squared to Grainger, who kept his cool in front of goal to seal the trophy.
Hebburn Town U23s XI: Hunter, Loch (Teixeira, 85') , Bada, Marley, Bone, Hudson, Solman (Stephenson, 21'), Carter, Murray, Gateshill (Stansfield, 62'), Maddison
Unused subs: Burns, Potts, Hobbs
Goals: Maddison (30')
Shotton Colliery XI: Beckett, Slater, Goundry, Walker, Tatters (Howe, 71'), Beeston, Winwood (Rookes, 52'), Hall, Kenney, Grainger, Bennett
Unused subs: Gillespie, Hart, Ball, Appleby, Cockroft
Goals: Bennett (49'), Grainger (90+3')
Referee: Matthew Morton
MOTM: John Murray
Attendance: 260