The Dane, whose last victory came at the 2017 Portugal Masters, started the day ten under par, four strokes behind 54-hole leader and twice-defending champion Tyrrell Hatton.
Bjerregaard began his final round on the 18th hole under a shotgun start, which meant he would finish the Championship on the iconic Road Hole.
The 27-year-old birdied the 18th and then made three further gains before the turn as he whittled down Hatton’s lead.
Birdies on the 13th and 16th holes saw him reach 16 under par, two ahead of Ryder Cup hero Tommy Fleetwood, who set the clubhouse target after a three under par round.
Hatton had a birdie chance on the last hole but had to settle for par, joining Fleetwood on 14 under. A bogey on the 17th was enough for Bjerregaard to win his second title, just a week after watching compatriot Thomas Bjørn captain Europe to Ryder Cup victory.
Finn Tapio Pulkkanen finished fourth on 12 under par, while Haotong Li and Andrea Pavan shared fifth place on ten under par. Li won the team competition with his partner Allen Zhang with a score of 35 under par.
“It was a great day. Obviously one of the best rounds I've played all year. I’ve played well recently and I've come close a few times, lost in a play-off in Switzerland, which obviously hurt. It feels really good. It's really nice to sit here right now and I'm going to enjoy this one, no doubt”, said Bjerregaard afterwards.
“I was looking at all the boards. It didn't really look like I had much of a chance to be fair. It looked like Tyrrell was going to run away with it. I just kept going about my business, and we knew the back nine was going to play tough.
“So I thought if I could throw in a few birdies there, I would still have a chance. I didn't rush it. I didn't try to make birdies; I didn't force them and they just slowly came and that one on 16 was really nice.
“It was obviously nice to start with 18 this morning because it's a good birdie chance. A nice way to get going, and make birdie there as I did, that's one early, so you can get a good start. But then playing 17, it's nice to know that you normally have 18 which is a good birdie chance, so if you bogey 17, you can get it back on 18. I didn't really have that.
“I was so delighted for Thomas (Bjørn). It's been amazing to see all the work that goes behind The Ryder Cup, and being close to him, it's been amazing to see how much work he's put in it. To win and the way they played the whole week, so delighted for him. I hope he's enjoying some down time now. I was definitely inspired, and I definitely want to make that team some day.”