Hey produced a second consecutive 66 to catch Shufflebotham, who added a 67 to his first-day 65.
But the Denbighshire man laid claim to professional golf’s oldest trophy in a sudden-death shootout.
“It’s the biggest win of my career,” said Shufflebotham after shrugging off the challenge from the chasing pack in normal time, edging to victory over Hey by settling the issue at the first extra hole.
Shufflebotham, 29, a former Welsh amateur champion whose home club is Prestatyn, reflected: “I was two under through five holes, but dropped a shot after three-putting the seventh before picking up a two-putt birdie on the long 14th.”
He was well prepared for his tilt at winning the Leeds Cup, explaining: “I spent some time working on my short game with Oliver Whiteley at Bramall Park, which helped a lot because he made it look simpler.
“I’ve also practised a lot with Richard Edwards at Oswestry for the last year.”
Shufflebotham revealed he had been struggling so much with his driver that he left it out of the bag.
“I just used two irons and a three wood, which kept me out of trouble,” he commented.
After earlier promising himself not to become aggressive, he reached the play-off hole in two as Hey bogeyed.
The trophy was presented to Shufflebotham by Neil Evans, Director of Resources and Housing for Leeds City Council in recognition of the club’s long association with the City of Leeds.
Leading scores: 132 Calum Hey (Shipley) 66 66, Jason Shufflebotham
(Denbigh) 65 67; 133 James Murray (Scarcroft) 68 65, Alex Belt (Snainton
Golf Centre) 66 67, Benjamin Thompson (Hazel Grove) 66 67; 134 Michael
Ramsden (Renishaw Park) 69 65, Tim Ford (Liverpool Driving Range) 69 65,
David Smith (Swinton Park) 66 68; 135 Ryan O’Neill (Penwortham) 70 65, David
Shacklady (Mossock Hall) 66 69, Jamie Howarth (Davenport) 66 69, Oliver
Whiteley (Bramall Park) 66 69.