The history books will etch Curtis Jones down as the match-winner though his goal was a massive deflection but the real hero was James Trafford after saving a penalty in the last minute.
Cole Palmer's free-kick on the cusp of half-time hit the Liverpool ace in the back, which saw the ball loop into the top corner.
But there was further drama when Levi Colwill was harshly adjudged to have fouled Abel Ruiz in the 96th minute after the referee went to VAR.
However, Burnley's new £19million goalkeeper Trafford stood firm to deny the Braga ace before making a second save to make history.
Chaos broke out that saw Morgan Gibbs-White and Antonio Blanco sent off on the touchline as Spain, who had 20 shots throughout the games.
READ MORE ON ENGLAND
Ashley Cole sent off as England goals sparks melee between benches during U21 Euros final
Why do England have so many players older than 21 Euro U21 Championship
However, Lee Carsley's men shut out all attacks as they had done all tournament.
Incredibly, England did not concede a single goal throughout the Euros in a testament to the defensive partnership of Taylor Harwood-Bellis and Colwill.
But it was not without controversy, particularly as England coach Ashley Cole was sent off.
After Palmer's goal, the Manchester City starlet raced towards the bench to celebrate.
Most read in Football
England U21 1-0 Spain U21 LIVE REACTION: Young Lions win U21 Euros after Trafford heroics
De Gea leaves Man United, Chelsea agree to sell Pulisic, Rice and Timber to Arsenal latest
Ashley Cole sent off as England goals sparks melee between benches during U21 Euros final
Man United transfer news LIVE: De Gea exit confirmed, £45m Onana deal imminent, Kane swap
However, he was met with an angry Spanish dugout and a fracas broke out between both sets of players and coaches.
Cole was shown a red card for his part, as well as a Spanish coach, while Oihan Sancet and Colwill were both booked.
This was an English team littered with top-tier stars, including Emile Smith Rowe, Angel Gomes and Anthony Gordon.
But Spain came into the match full of confidence as the tournament's top scorers, led by Braga's Ruiz.
Nevertheless, the Young Lions proved resilient in the end and could have been 2-0 up after six minutes.
Gordon had an excellent chance after spinning his way toward goal but Arnau Tenas kept him out.
The Newcastle forward then had another opportunity before setting up Morgan Gibbs-White, who was an inch away from tapping in an open goal.
Palmer was the man brought down before half-time and it was his set-piece that saw England ultimately claim victory.