Turkey led 1-0 at halftime thanks to a goal in the 25th minute by Omer Guleryuz.
Although the dominant display from the Turkish team continued until the final minute, England's Ray Westbrook still managed to tie the game in the 50th minute.
However, Turkish team captain Osman Cakmak scored two minutes later to give Turkey the title.
Turkey's President Recep Tayyip Erdogan congratulated the Turkish amputee team on Twitter. "I congratulate our national amputee football team for becoming European champions by beating England. Turkey is proud of you!" he said.