'Los Blancos' have been out of sorts of late and their poor form continued as they crashed to an embarrassing defeat at the Estadio de Mendizorroza.
Julen Lopetegui's side continued to look goal-shy going forward and they were punished deep into stoppage time as the hosts claimed a shock win.
Jony, who was a bundle of energy throughout, forced a late corner down the left, with the Basques taking full advantage.
The Sporting Gijón loanee whipped in the set-piece, with Rubén Soriano meeting it at the far post.
His header was kept out by Thibaut Courtois, but the Belgian was powerless to prevent Manu García from stealing in ahead of Sergio Ramos to nod home from close range and send the Alavés faithful into raptures.