Germany international Kroos, 24, is 11 La Liga games and four UEFA Champions League appearances into a six-year deal with the Spanish giants.
The Bayern Munich youth graduate scored his first goal in a Real shirt in their 5-1 drubbing of Rayo Vallecano on Saturday, helping Carlo Ancelotti's men consolidate top spot in the league.
Heynckes coach Kroos in his caretaker role at the Allianz Arena in 2009, and again from 2011-13, and the 69-year-old hailed his former charger's beginning to life in the Spanish top flight.
"Kroos is playing magnificent football," Heynckes told Perform.
"It's his destiny to play there. He has a leading role as a playmaker in the midfield of Real Madrid and that's a huge achievement because only world class footballers are playing there.
"The team accepts him, he's wonderfully integrated.
"You cannot play the position Kroos plays in defensive midfield, besides Luka Modric, better than he does.
"I called him, I sent him messages to congratulate him.
"It's really fantastic, particularly if you consider the pressure there is in Madrid."
Former Real boss Bernd Schuster - a countryman of Kroos' - said he is not surprised by his influential start to his Madrid career.
"Kroos is everything I was expecting because he is an intelligent player," Schuster said.
"That's a very important attribute in this game. He has it all as a player but I still think that his ideal position is a bit more advanced, at least that's where I like him because he can exploit all conditions.
"You have to adapt the needs of your players to the team. Kroos is adapting fast because of his quality and intelligence. He's got a good understanding with Modric, who is another like him who could play more advanced.
"Because Kroos is often so far back, it's difficult for him to use some of his qualities, like making the final pass or shooting.
"German players have always been good long-range shooters... we like having a shot."
