Nico Williams’ effort on the counter had handed Spain the lead just over one minute into the second half despite Rodrigo being substituted at the break.
La Roja had looked the more likely to score after a cagey opening 45, but former City man Cole Palmer came off the bench to draw England level with 15 to play.
But it was another substitute who would land the decisive blow, with Mikel Oyarzabal stealing a yard in the England box to tap home the winner as stoppage time approached.
It means Rodrigo adds another trophy to his remarkable haul, while it was another final heartbreak for Walker, Stones and Foden despite another gutsy display.
Spain had quickly established themselves as potential title candidates at Euro 2024, while England had gradually grown into the tournament, winning just twice inside 90 minutes en route to the final.
But while their journeys through the Euros had been different, the two sides couldn’t be separated in the early exchanges in Berlin.
England were thankful to Stones for some excellent one on one defending to deny Williams a sight of goal early on, while a timely block from Rodrigo thwarted Harry Kane late in the half, but genuine chances were at a premium.
Indeed, the first save that either goalkeeper had to make came in first half stoppage time, when Foden’s stretching volley at the far post from a free-kick was claimed by Unai Simon.
Rodrigo was replaced at the break by Martin Zubimendi at the break due to injury.
It was a blow for the Spanish, but they would take the lead inside two minutes of the restart when Lamine Yamal released Williams on the left.
The winger’s run had gone untracked and, despite Walker’s best efforts to get back, he confidently side-footed the ball back across goal and into the net.
England were lucky not to find themselves two behind inside three minutes when Dani Olmo had a sight of goal, but the midfielder snatched at his effort with the goal gaping.
After an out of sorts start, Spain were beginning to assert their dominance.
First, Williams fired wide from distance just moments after Stones had cleared Alvaro Morata’s effort off the line, before Pickford was called into action to tip a Yamal strike wide of the post.
With Kane brought off on the hour for Ollie Watkins, Walker took on the captain’s armband as Gareth Southgate looked to roll the dice.
But it was a different substitute, former City man Palmer, who drew the teams level with 20 to play.
Picking up Jude Bellingham’s cutback on the edge of the Spain box, the midfielder guided an inch-perfect effort into the bottom corner to set up a grandstand finish.
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Pickford and Yamal’s individual duel continued apace, with the former once again parrying the 17-year-old’s effort away from danger as the game ticked into the final ten minutes.
But the England stopper would be beaten with five to play, when Marc Cucurella’s ball in from the left was tapped home by Oyarzabal.
In need of a goal, Southgate opted to withdraw Foden as stoppage time approached in place of Ivan Toney, with the Three Lions going agonisingly close soon after when Declan Rice and Marc Guehi both saw headers cleared off the line.
But it wasn’t to be for our English City trio, with Spain holding on for a record fourth successive European crown.
Congratulations to Rodrigo, and commiserations to Kyle, John and Phil.
