His side have been irresistible since late October and have now gone 19 matches unbeaten in all competitions.
Going into Tuesday's game they had kept six consecutive clean sheets and have leaked only seven goals in 22 Bundesliga matches so far this season.
Asked if Arsenal had the quality to score three times in the Allianz Arena next month, Heynckes was diplomatic but spoke with the confidence of a man who has his side running like a well-oiled locomotive.
"Arsenal are a good team and we will be taking the second leg very seriously," said Heynckes, who will hand the baton to former Barcelona coach Pep Guardiola next season.
"In this season it's very difficult against us. We have 22 games and conceded just seven and that's just amazing.
"You can see it's very difficult to score against us and my team is always in the position to score two or three goals so I do think we have chances to progress to the next round."
First half goals from Toni Kroos and Thomas Mueller and a late third from Mario Mandzukic after former Bayern player Lukas Podolski had briefly given the Gunners hope, underlined the German club's superiority.
Once they fell behind in the seventh minute Arsenal seemed fragile and Bayern never looked like squandering the chance to emulate Schalke who also won at the Emirates this season.
"We played against a team with a lot of class. They played much better than us in the first half," said Wenger, who is coming under increasing pressure as an eighth successive trophy-less season looms.
"They are a team with quality and are very efficient. They are a good side. Congratulations to Bayern.
"Let's not hide the truth, it will be very difficult but we'll try to make the impossible possible. We have to go there and play like we play at home and try to change the score.
"The third goal of course makes it very difficult but we have to try."
Such is the quality in the Bayern ranks that former Chelsea and Real Madrid winger Arjen Robben was only among the substitutes along with Mario Gomez.
Robben, who came on just past the hour, said Bayern's game plan had been to steal Arsenal's early thunder.
"Tonight we made a very big step towards the quarter finals but we need to stay focused on our own game," he said.
"We expected a very big start by Arsenal here at home with the fans behind them and we warned each other that we had to be there from the first minute because there will be a storm at the Emirates Stadium."
The storm failed to materialise though and, despite midfielder Jack Wilshere working overtime to try and spur his team-mates on, Arsenal were overwhelmed.
"We didn't start great and that's been a thing for us this season," Wilshere said
"In the second half we stepped it up and it's unfortunate we didn't do that in the first half. I'm not sure why, maybe it's a bit of nerves or anxiety because we show what we can do when we play. We will look at it and try to put it right."