This occurred just before the trophy lift, following Tottenham's 1-0 victory over Manchester United in the final.
UEFA President Aleksander Ceferin was seen discussing the issue with colleagues as he handed out the remaining medals.
Son was the last player to greet Ceferin, briefly chatting and embracing before proceeding to the stage without a medal.
UEFA apologised for the shortage of medals, which they blamed on “unexpected discrepancy in the player count”, but added affected players were given medals in the dressing room.