Heynckes warned the bad run of English teams in the top European competition this season should not be any indication of the real threat that Arsenal, trailing 3-1 from the London leg, will pose on Wednesday.
"There is always change in the Champions League," Heynckes told reporters. "Now it's Italian and German clubs that seem to be back in fashion this season. These are changes that revitalise European football."
Title holders Chelsea, Manchester City and Manchester United have already been eliminated from the competition.
The Bundesliga leaders, in stark contrast to their English opponents, have enjoyed a scintillating season and are in the running for three title.
Heynckes, however, has urged his players to remain grounded despite the fact that only two teams have advanced after losing the home leg of a Champions League knockout round match.
"I have no interest in dividing up the skin before I kill the bear," Heynckes told reporters on Tuesday. "My team is not listening to those saying we are the best team in Europe at the moment.
"There are several top teams and you have to confirm that status in every game. We have to stay modest and that is how we need to continue.
"We should not allow to be influenced from the outside because in order to be called the best team you have to confirm that internationally," said the 67-year-old coach who will make way for Pep Guardiola at the end of the season.
The Bavarians have twice in the last three years reached the final of the competition but their last Champions League trophy victory was 12 years ago.
"I know (Arsenal coach) Arsene Wenger well and I have high respect for him as one of the top coaches in Europe. Arsenal will come here and will try out everything they can think of," said Heynckes, who won the Champions League with Real Madrid in 1998.
"We had a super day in London in the first leg but this is the Champions League and Arsenal are not just any team," he said.
"Arsenal have played successful football for many years and my experience says you have to be 100 percent there. My players see it exactly that way and I have no doubt that the 3-1 result plays absolutely no role in their mind any more."
Bayern will be without suspended Bastian Schweinsteiger and Jerome Boateng while Franck Ribery has been ruled out with an ankle injury.
Dutchman Arjen Robben will start in place of Ribery on the wing, Brazilian Luiz Gustavo will replace Schweinsteiger and Daniel van Buyten is expected to slip into the central defence for Boateng
The Germans are expected to let Arsenal come forward and use the space available for quick breaks as they eye their third quarter-final spot in four seasons.
"We start from 0-0 and it is they who have to score three times," captain Philipp Lahm told reporters. "For us that is good because they have to be more offensive. They have to pressure from the start."
"Obviously they have to attack and we will work hard in the back to create spaces. If we pull back a bit it means we will have more space up front and that will be hard for Arsenal," said Lahm.
"They cannot completely open up in defence but they still need to score three goals here."