It gave them a three-shot margin over three rivals – Teesside, Harrogate and Sheffield.
South England Boys’ champion Jack Maxey, of Hornsea, led the way for the eventual champions with rounds of 71 70, the lowest 36-hole tally of the day.
His East Riding team-mates were Lewis Hunt (77 75), Nick Raybould (78 74), Andy Woodhead (76 78), Dan Digby (82 73) and Leigh Gawley (79 77).
Bradford had led the way at the halfway point with a 457 first-round aggregate.
It gave them a one-shot lead over Harrogate and Sheffield and two over Leeds.
But East Riding came storming through from six shots back to claim the trophy.
Bradford slipped right to the back of the pack as four of their players carded scores in the 80s.