Group Captain held off the challenge of Resonate to win the November Stakes on the final day of the 2006 flat season at Windsor.
Moore rode 180 winners over the season
Ridden by Richard Hughes, Group Captain battled well in the closing stages to overhaul his rival and claim victory.
Newly-crowned champion jockey Ryan Moore had to be content with third on Book Of Music.
Moore, 23, became the youngest champion since Pat Eddery in 1974 and Eddery who presented Moore with his trophy.
"I have been real lucky and everything went perfect all year through," he said. "I have had a lot of help from Mr (Richard) Hannon and my family and I have been very lucky."
"I am delighted for him as he is a great rider and works hard," added 11-time champion Eddery.
"He went all over the country from Brighton to Hamilton in search of winners and he deserves every bit of his success and we have got a real champ."
Stephen Donohoe was also crowned champion apprentice with 44 winners while Sir Michael Stoute won his ninth champion trainer's title.
Meanwhile, Parsons Legacy ended Richard Johnson's week on a good note with victory in the Badger Ales Trophy Chase at Wincanton.
Johnson had a disappointing time at Exeter on Tuesday when his mount Out The Black stumbled and fell with the line at his mercy.
But the Philip Hobbs-trained horse, who went off at 14-1, took over the lead with three fences left and easily held off the challenge of Preacher Boy.
November Stakes (Windsor)
1. Group Captain (R Hughes) 10-1
2. Resonate (C Hayes) 20-1
3. Book of Music (R L Moore) 13-2
4. Castle Howard (Debra England) 50-1
Badger Ales Trophy Chase (Wincanton)
1. Parsons Legacy (R Johnson) 16-1
2. Preacher Boy (P J Brennan) 14-1
3. Nil Desperandum (T Scudamore) 16-1