The German side took the lead just after half time and looked like they would secure a memorable win before Arsenal were awarded the spot kick.
Former Bayer Leverkusen forward Kai Havertz stepped up to break the hearts of his old club and rescue the draw.
Speaking after the game, Hjulmand was adamant it shouldn’t have been awarded, saying: "I have mixed feelings.
"It was a very good performance against a top team – of course we are disappointed with the last scene. A 1-0 would obviously have been much better than a 1-1. I don't see a penalty there, but that's how it is.
"We are going to London with hope. I believe there is a lot of pressure on Arsenal. We must and we can deliver another strong performance.
“We have to seize the opportunity and are looking forward to Tuesday. But for now, Bayern is what counts."