The Real and Spain captain, who insists he accepts the decision, had not been dropped from the team for 10 years, but Mourinho opted for Antonio Adan, 25, instead for the game at La Roseleda Stadium.
The subsequent 3-2 defeat to Manuel Pellegrini’s side left Real 16 points adrift of La Liga leaders Barcelona after four league losses this season.
Mourinho is facing serious questions about his immediate future at the Bernabeu, but was surprised to be asked about it after the defeat to Malaga.
The cracks are starting to show in Mourinho’s reign at Real, and his recent erratic behaviour as recounted by Marca writer Anton Meana serves only to underline the pressure he is under.
The factions within the Real camp are beginning to deepen further, and the dropping of Casillas, such a talismanic figure for the club, does appear to point to problems behind the scenes.
This is nothing new to Mourinho and Real, though, after reports of a rift between manager and players emerged last season too.
But that was in a Real team leading La Liga and on course for the championship.
This season, the situation is somewhat different, with Barcelona cruising towards regaining their title.
Mourinho is no stranger to confrontations, although winning them is a different issue altogether, as Chelsea supporters will remember from his eventual demise against the equally bloody-minded club owner Roman Abramovich.
But will Mourinho still be in the Real Madrid hot seat for the Champions League last-16 quarterfinal first leg against Manchester United in February?
There should be little doubt he will be.
Mourinho loves the limelight, and the tie against United affords him one of the biggest stages of all in which to revel. He wouldn’t miss it for the world. It would also be a golden opportunity to put himself in the frame to replace Ferguson.
And to whom would Real turn if Mourinho did leave the club before the United ties?
Rafael Benitez recently seemed to hint at a move to the Bernabeu in the summer, but he is tied to Chelsea until then. Mourinho was swift to react to those comments, though, refuelling his feud with the Spaniard from their days in England together.
Borussia Dortmund's Jurgen Klopp will also be on the club’s radar after rebuilding the German side and still winning successive Bundesliga titles in the process. But Klopp is unlikely to want to leave midseason.
Germany manager Joachim Low is a favourite for the role but has distanced himself from the post recently.
So, options are limited if either Mourinho or the Real hierarchy decide to cut their losses before the United tie.
And with Mourinho in the opposition dugout, Ferguson will dismiss any notion that rifts behind the scenes will detract from the danger his side still face.