The match could have gone so differently for Real Madrid.
The result means Calleja's team climb to fifth place in La Liga, and are now only a point behind Madrid, who have a game in hand over the triumphant visitors.
"The first thing I'll say that it's hard because we did everything", he said after the game. Sport focused on the troubles in front of goal of Ronaldo, who missed numerous chances at the Santiago Bernabeu before Pablo Fornals' magnificent late victor for Villarreal, its first victory there. Asenjo punched away a long-range blast from Marcelo, got his fingertips to a Cristiano Ronaldo free kick, forced Ronaldo to hit wide one-on-one, saw Ronaldo hit the outside of the post on another chance, blocked a Ronaldo shot from six feet out and parried away a rocket volley from Toni Kroos.
Ronaldo has publicly stated many times his love for United remains and AS claim that the player now believes that Old Trafford would be the "ideal" place to continue his career.
Ronaldo almost scored from close range just before halftime, but his shot was brilliantly saved by goalkeeper Sergio Asenjo.More news: Wales name Giggs as manager on four-year deal
Gareth Bale had a goal disallowed for offside early in the first half.
Even though Spurs are adamant that they are not going to let Kane leave, the player may decide otherwise if Spurs can't promise any trophies and if Madrid comes knocking.
Shot accuracy was just 39% and they missed 2 big chances as well.
Keylor Navas did well to save the first attempt but Fornals placed the rebound just over the outstretched fingertips of the Costa Rican keeper. Fornals picked up the loose ball just outside the area and chipped it over the goalkeeper for the stunning victor.
The gap could have increased to 19 points if the Catalans triumphed against Real Sociedad in last night's late game.
Spain global Rodrigo Moreno struck the second in the 64th with the help of a huge deflection off Depor defender Pablo Mosquera.