Uefa has also issued a partial stadium closure after crowd trouble in the recent meeting with Manchester City, while Napoli and Porto have also been punished for fan unrest
Uefa launched an investigation after City's 1-0 win in the Youth League round-of-16 meeting on February 26 was marred by alleged racist remarks directed at Devante Cole, the son of former Manchester United and England striker Andrew Cole.
Europe's governing body has since decided there are grounds to take action against the Spanish club's youth sector, prompting the decision to issue a fine and order a section of the ground to be closed for the next home match in the competition, as confirmed on their official website.
Meanwhile, Italian giants Napoli have been fined €26,000 after crowd trouble in the recent Europa League meeting with Swansea City.
Uefa revealed action was taken as a result of "insufficient organisation, illicit banners and setting off of fireworks" in the 3-2 second-leg victory over the Welsh club.
Eintracht Frankfurt have also been punished with a €30,000 fine after fireworks were thrown from the stands in their Europa League encounter with Porto on Febrary 20.