Ridden by William Buick, Mischief Magic was boxed in on the rail turning for home. However, the colt was threaded through the leaders to lunge in the final yards.
Showing an impressive turn of foot, the bay streaked past Karl Burke's Dramatised to prevail in a British one-two, with the Richard Hannon-trained Persian Force back in fourth.
Appleby told Sky Sports Racing: "I knew they were going to go hard.
"William has been in such great form and riding with such confidence, I could see what he was doing.
"He was trying to get him on his lead and he got him on his lead on the back turn there, I could see where he was trying to angle out and just got pushed back in again.
"I don't think it did the horse any harm because as I said to Will, just give him gaps, he just needs daylight and he might just have a chance.
"A great ride by William, I'm delighted. It's great to be back."
Mischief Magic was last seen finishing fourth to the now-retired Blackbeard in the Middle Park Stakes at Newmarket in September and Appleby felt that had been a good prep outing.
The Godolphin trainer said: "Going into the Middle Park, we were always mindful that it was a stepping stone to this race and that he was pitching with the best colts in the UK.
"The plan was for him to sit a bit closer but after missing the break, Will let him find his legs and it was a great ride.
"He's such a willing horse and it's also great that he's a homebred.
"He will have the winter off and with his scope, I can see him developing into a contender for the Commonwealth Cup at Royal Ascot."
The Platinum Queen was widely expected to take a hand in the finish for Richard Fahey after her Group One success in the Prix de l'Abbaye last time, but she was under pressure from some way out in the hands of Hollie Doyle and finished down the field.
Fahey said: "I was disappointed with her run. Nothing seemed to go right and Hollie said she felt a bit flat.
"She will have a well-deserved holiday now.
"Hollie said she got more worked up today than she had done before and I think it was all a bit of a shock to her system.
"She jumped well but one came around her outside and from then it was not going right for us."