In a dramatic finale in Batumi, Spain captain Abel Ruiz had a 99th-minute penalty saved by Manchester City goalkeeper James Trafford to preserve England’s record of not conceding a goal all tournament.
Lee Carsley’s men won all six games in Georgia and Romania to continue a golden age for England’s youth sides.
The Three Lions are also reigning European champions at under-19 level and won the under-17 and under-20 World Cups back in 2017.
There was a hint of fortune about the only goal as the ball struck Jones from Cole Palmer’s free-kick in first-half stoppage time and looped into the far corner.
Spain did have the ball in the net after the break when Ruiz headed home only to be denied by the offside flag.
The Braga striker had an even better opportunity 20 minutes from time when he headed wide with the goal gaping.
England could also have put the five-time winners away before an incredible ending as Arnau Tenas made fine saves to deny Jones and Noni Madueke a second.
But they needed Trafford – who has been linked with a £19 million ($24 million) move to Premier League newcomers Burnley — to produce some heroics at the death.
He parried Ruiz’s spot-kick and a follow-up effort from Aimar Oroz to spark wild celebrations among the England players and coaching staff.
The drama did not end there as Morgan Gibbs-White and Antonio Blanco, who had already been substituted were both shown red cards.
Earlier, former Chelsea and Arsenal left-back Ashley Cole, who is part of the England coaching staff, had also been dismissed from the bench.
But in front of the watching England manager Gareth Southgate, they held on to go one better than the senior side managed in losing the Euro 2020 final two years ago.
AFP