The Germany international, who established himself in the Bayern first-team as a product of the academy, started for Real and played for 114 minutes until he was replaced by Mateo Kovacic in extra time.
Controversial refereeing decisions overshadowed the Champions League clash in the Spanish capital, with Cristiano Ronaldo scoring two offside goals and Bayern's Arturo Vidal harshly being sent off with minutes left of normal time.
Real went onto win the tie 4-2, progressing into the final four of the competition with a 6-3 aggregate.
But it was the moment Kroos shared with the Bayern fans which he will have enjoyed most.
Following the tie, with the Bayern fans still in the stands at the Bernabeu, Kroos took to the field with his young son and a football.
Kroos junior proceeded to score in the empty net, with the Bayern fans cheering loudly in support of the youngster, with his father sharing the video on his official Twitter account.
"Thanks to all @fcbayern supporters who made it such a special night for my son," he said.