Bayern's bid to reach the Champions League final, which will be staged at their Allianz Arena next May, could hardly have got off to a better start after Kroos' seventh-minute opener - added to by Rafinha in the second half - set them up for what turned out to be an easy night in Spain and Heynckes believes people are now finally taking note of the Germany international.
"Toni Kroos now has a lot more self-confidence and he is in a great condition physically," said Heynckes, who took Kroos to Leverkusen on loan from Bayern while he was in charge there.
"He has my confidence and my total support and his team-mates are now starting to realise what an excellent footballer he is.
"He played an absolutely fantastic game."
However, it was not all good news at El Madrigal for Bayern as they lost Daniel van Buyten and Mario Gomez to injuries.
"Van Buyten has a problem with an Achilles tendon and, as we know, Mario Gomez had to pull out of the national team and he still has problems with his groin," Heynckes added to Sky television.
"I hope that it is not so bad that he cannot play on Sunday. We will just have to wait and see."
Gomez, who has scored seven goals in his last two league matches, is therefore a doubt for the Bundesliga clash at Schalke and he is hoping for a miracle cure to enable him to carry on that remarkable scoring record.
"In the condition I am today (Thursday), then there is definitely no chance I can play," he admitted.
"I really don't know what is wrong. All I do know is that I had a lot of pain in the groin region and we have got to take a look at it.
"The doctor will examine me today (Thursday) and then tomorrow in Munich."