Cardiff last week signed Dimi Konstantopoulos on loan to compete for a place but it looks like the keepers shirt will be his by default.
Heaton helped keep the score down at The Emirates with a string on fine saves but his chance of keeping the shirt has been taken from him.
"I felt something after about 35 minutes of the Arsenal game, but I didn't think it was that bad, so I didn't mention it to the staff at half-time," Heaton told the Echo.
"But, towards the end of the game, and the last five minutes in particular, I felt it stiffen up.
"So I went back to Manchester to see the medical staff and find out what the problem was.
"I still didn't think it was too serious, but the physio had a look and decided I should have a scan.
"An hour later I'm told that I'm going to be out for five weeks. I'm absolutely gutted."
Heaton was set to fight with Konstantopoulos for a startng place but the on loan Man Utd keeper has been left on the sidelines.
"It's so frustrating because I've had to wait for my chance and now this happens," he continued.
"But we have talked about mental strength at the club and that's been important to me in the last couple of months.
"And I've got to be strong now because this is one of those things that happens in football.
"One minute you are OK and you get your chance, the next this happens and you're out for five weeks.
"I was just delighted to get my chance at Arsenal and I was pleased with the way I played.
"I was looking forward to playing on Sunday because it's such a big game.
"It's disappointing not to be playing, but I will get behind the boys and hopefully we can get the three points.
"All I can say is that I will make sure I am as fit as possible when I come back again."
Heaton believes the competition for places is good.
"I know that Peter, Dimi and I all want to be No 1 at this club," said Heaton, who signed a one-season loan deal at Cardiff last summer.
"I know it's a bit of a cliche, but competition does keep you on your toes.
"Nobody can get comfortable here and that's the way it should be, it really brings the best out of you.
"I have to say Martyn Margetson (goalkeeping coach) has been superb and Peter has also been fantastic to me.
"I had no complaints whatsoever with Peter being in front of me and I was supportive of him when he was enjoying a run in the side.
"Peter was exactly the same when he was injured and I got my chance.
"My aim on Monday was to put in a decent display and although we lost I think I did that.
"That's why it's such a blow to get this injury now, but hopefully I will be back as soon as possible."