Old Persian punched his ticket to next month's William Hill St Leger with victory in this Group Two prize, while the Melbourne Cup beckons for the runner-up.
Appleby who also has Saturday Newbury winner Hamada for the Melbourne Cup, said: "The two horses came here in great order. I put a line through Old Persian's run in the Irish Derby. We might have backed up quick enough after Royal Ascot, but I always felt the horse was going there in great order.
"It was more the fact the race didn't pan out as we expected as they slowed up in front and we weren't in the right position.
"The horse needed a break from there and he had a nice, little break. The team have got him back well and we were confident coming into today. He's bred to get a trip and he galloped out strongly.
"Cross Counter came onto the scene later on and this wasn't his main target, but on the back of his victory at Goodwood he put himself forward to be in the picture for Australia (Melbourne Cup).
"I didn't want to take him down as a three-year-old and give him a prep run there. I thought it would be easier if I could get a prep run in here and go down there as a fresher horse and run him off the plane.
"Really, it couldn't have worked out any better. I know the betting didn't suggest that, but Old Persian can head on to the St Leger now and Cross Counter can do what we always expected him to do and go to Melbourne for the Cup."
He added: "I think we have a nice team going down to Australia, but it just depends how well they travel.
"That's their biggest challenge and if they turn up as they would on this side of the water they are going to be big players."
Michael Hussey set a decent gallop aboard Nelson in the early stages, with Wells Farhh Go, the only Yorkshire-trained horse in the field, Old Persian and Cross Counter not too far away.
The race was wide open three furlongs out, where Wells Farhh Go was the first to commit, but the Godolphin pair soon dominated proceedings.
Sent off at 7-1, Old Persian kept finding for James Doyle and returned to the form of his win in the King Edward VII Stakes, following defeat in the Irish Derby, as he kept his stablemate at bay by a head.
The Aidan O’Brien-trained Kew Gardens made up plenty of ground from the rear to take third place, a length and a half away.
Kevin Buckley, Coolmore's UK representative, said of Kew Gardens: "He's run a great race, he's just been beaten by the penalty.
"It's nice to see him come back from his little break after his race in France in such good form.
"He should step up on that perfectly in time for Town Moor (Leger).
"Ryan (Moore) was very happy with him."
Tim Easterby said of Wells Farhh Go, who was fourth: "I'm very happy with that, he just needs one-mile-six or two miles on soft ground and he'll win.
"Back on quicker ground and over a mile and a half he's just been found out today - when he was asked to quicken he was just climbing a bit.
"The first three all look like they'll improve for going up in trip, to be fair.
"There's also a race in France just for three-year-olds over one-mile-seven we can look at."