Native Trail was sent off the 5/4 favourite under William Buick but it was the Godolphin second string Coroebus who prevailed by three-quarters-of-a-length at 5/1 for James Doyle.
Derby favourite Luxembourg put up a fine performance to be third over what connections feel will prove an inadequate trip and bookmakers immediately cut his odds again for that race at Epsom in early June.
Native Trail proved his well-being with a comprehensive victory in the Craven Stakes two and a half weeks ago weeks ago, while Coroebus was making his first competitive appearance since winning the Autumn Stakes over the course and distance in early October.
With the pair drawn on opposite sides of the track, they raced wide apart for much of the straight-mile contest, with Buick the first to get vigorous aboard Native Trail nearest the stands side.
Doyle, on the other hand, was able to wait until the furlong marker to pop Coroebus the question and he found plenty racing out of the dip.
“Coroebus is a homebred and by Dubawi and I’d like to think I know the Dubawis by now - I’ve had enough of of them through my hands - and he’s shown us all the right signs,” said Appleby, who became the first trainer in 20 years to saddle a one-two in the race.
“It was always going to be hard call for William to get off Native Trail and get on him and it’s great for James, who is an integral part of the team and for him to have his first English Classic winner is fantastic. For us to be able to provide it is even more special.
“I don’t think William will have any excuses - he was potentially beaten by a better horse. I could see James was travelling for fun and that’s what this horse does - they can’t go quick enough for him.”
“I’m delighted, delighted for the whole team and most importantly His Highness Sheikh Mohammed and Team Godolphin.”
Additional reporting by PA.