German publication Bild suggested during the week that Heynckes had confronted the star striker over an apparent decline in his training standards.
The 29-year-old, who has been heavily linked with a move to Madrid, failed to fire in the Champions League loss to Los Blancos last week and sat on the bench as Bayern beat Eintracht Frankfurt 4-1 in the Bundesliga on Saturday.
However, speaking after that match, Heynckes reiterated the one-on-one conversation was purely motivational, and insisted Lewandowski would not be overlooked for the semi-final second leg.
"I can only tell you what I also said in the press conference yesterday - that I had a good talk with Robert Lewandowski," the Bayern boss said.
"But I did not say anything about the content of it. For me, Robert Lewandowski is a world-class player and please do not think that I will ignore him for Tuesday.
"So far he managed to score 39 goals in all competitions. This is a mark of which most of the forwards in Europe are dreaming of.
"We should, first of all, await the game on Tuesday. It was a very positive talk and he always trains well. That’s why I don’t understand [the report]."
Jupp #Heynckes after #FCBSGE: "I'm very happy with my team's performance. Especially in the second half, we played well and were very efficient. Something we were lacking on Wednesday." #FCBSGE pic.twitter.com/bCfyosjoRm— FC Bayern English (@FCBayernEN) April 28, 2018
Lewandowski was among eight players to drop out of the starting XI for the visit of Frankfurt, who were led by Niko Kovac.
While Heynckes lauded the "remarkable" performance of the Bavarians' youngest line-up since 1971, his impending successor rued the visitors' vulnerabilities as they conceded three times in the final 15 minutes.
"The quality that Bayern still had on the field was enough to score goals," Kovac said.
"The result is a bit too high for me, but also deserved because of my team's naivety."