The Germany international remains a pivotal player for Madrid almost four years later and gone on to dominate Europe even further as he chases a third consecutive European crown with Zinedine Zidane's men this season.
Often regarded as one of the game's top midfielders, the World Cup winner is still sorely missed by former side Bayern, according to Sammer, who says he tried his best to keep him.
"Sometimes there are situations that you have to analyse honestly in retrospect," the ex-Bayern sporting director said in an interview with Sport Bild , which hosted Kroos as a guest editor this week.
"Who can say they have done everything right in life? Maybe Bayern Munich would have won the Champions League more often with Toni or at least reached the final.
"I can say today that, in my role, it was a mistake to let Toni go. I was sitting on Toni's couch trying to change his mind.
"I've been able to work with him for a long time and have known him since he was 16 or 17.
"His departure didn't shake Bayern, but when you talk about whether it was good or bad to let Toni go, you have to say it was bad, very bad.
"But for Toni's personal development and value, the change was definitely the right one."
Kroos has made 29 appearances in all competitions for Madrid this season, scoring four times, and is contracted to the club until 2022, althoug he has been linked with a summer move to Manchester United.