With Bayern reportedly keen to take up a €42million option to sign James Rodriguez on a permanent deal, there have been suggestions Madrid could use the opportunity to negotiate for Lewandowski.
"[Chairman] Karl-Heinz Rummenigge has already said it: with Robert, Real Madrid have no chance at all," he told a news conference.
Heynckes was less forthcoming with his views on the futures of Franck Ribery and Arjen Robben, whose contracts expire at the end of the season.
"I have my opinion on Ribery and Robben. But I will hold back here with my recommendations," he said.
"The club will know what they are and will decide in due course."
Earlier on Monday, Rummenigge denied reports Bayern have already decided to sign James on a permanent basis, although he praised the Colombia star for his recent form.
Heynckes also admitted he does not know whether his two-year loan deal will be turned into a transfer, but he thinks James is transformed from the player who struggled under Carlo Ancelotti before the Italian's departure in October.
"Of course, I knew him before he came to Bayern," he said. "When I took over the team in the autumn, he wasn't physically fit. He is stronger physically now, he's a completely different player.
"He has integrated into the group and he feels very good. He'll definitely play at Bayern in the coming season but Bayern must decide what happens beyond that."