It came just hours after Barcelona were forced to play their game against Las Palmas behind closed doors due to fears of crowd safety.
In the 12th minute of the game at the Bernabeu, swathes of the Rojigualda appeared all around the Bernabeu as Madrid fans decided to show where their support lies.
The Spanish government, who are based in Madrid, has said that the Catalan referendum vote is "illegal".
It had led to fights breaking out around Catalonia between police and pro-independence supporters.
SunSport reported earlier how Barcelona, who defeated Las Palmas 3-0 in their La Liga clash, showed their support for the Catalan independence referendum by posting the word 'democracy' on their scoreboard.
Their La Liga game against Las Palmas was played behind closed doors as the club decided it wasn't safe in light of the violent protests going on throughout the region.
And after the Barca players came out for the pre-match warm-up wearing shirts in the colour of the Catalan message, a defiant message was lit up on the scoreboard.