Bayern's chief executive Karl-Heinz Rummenigge was quoted in Munich's Abendzeitung as saying the club would offer Heynckes a new role next season.
"Jupp Heynckes has done a fantastic job here at Bayern," he was reported as saying. "He's one of the best trainers in Europe. We have offered him a chance to carry on at Bayern."
However, interviewed by Sky Sports just before the Bundesliga game against Fortuna Duesseldorf, Heynckes simply smiled and said "No" when he was first asked about the report.
He then added: "That's a surprise to me. It's the first I've heard about it. It's not correct."
Heynckes was brought back for a third stint as Bayern coach last season when he was given a two-year contract.
But his comeback was a disappointment as the Bavarians, Germany's biggest and brashest club, finished as runners-up in the Bundesliga, German Cup and Champions League.
This season, however, Bayern have been outstanding.
They have a 20-point lead at the top of the Bundesliga, have reached the German Cup semi-finals and are well-placed to reach the Champions League quarter-finals next week after winning 3-1 at Arsenal in the first leg of their last 16 tie.
Before Bayern announced former Barcelona coach Guardiola's appointment, Heynckes had remained quiet over whether he wanted to continue in the post and there had been suggestions he would be offered an extension.
Bayern are often known as FC Hollywood due to their array of expensive signings and big-name directors who, as well as Rummenigge, include former German internationals Uli Hoeness, the club president, and sporting director Matthias Sammer.
Bayern made it 10 wins out of 10 this year when they twice came from behind to beat Duesseldorf 3-2 on Saturday, Jerome Boateng heading the winner four minutes from time.