It takes the Sir Henry Cecil-trained colt's record to 13 wins from 13 races.
Despite stepping up in distance to 10 furlongs for the first time, the world's top-rated horse (1-10) powered through the field to take a record eighth consecutive Group One victory.
The Tom Queally-ridden four-year-old won the £725,000 race by seven lengths.
Frankel has now surpassed Rock of Gibraltar's mark of seven Group One wins in a row.
Cecil, who has battled stomach cancer since 2006, was at York to see his prized asset extend his perfect record.
"It's fantastic and it's great for Yorkshire, they're very supportive of racing and deserve to see him. [It helped me feel] 20 years better," he said.
Godolphin's Farhh (10-1) finished in second place, ahead of Ballydoyle's St Nicholas Abbey (5-1) in third.
Having been slowest out of the gate and then finding himself caught in the middle of the field in the opening stages, Frankel came past St Nicholas Abbey on the near side with two furlongs to go and then eased to victory in the Ebor Festival's showpiece race, sponsored by Frankel's owner Khalid Abdullah.
"Every man and his dog had his penny's worth as to where he should run and what he should do, but to run him in the owner's race and to go and win 13 from 13 speaks for itself," said Queally, who has mounted the Newmarket horse to each of his remarkable wins.
Queally said that he was prepared for the two Ballydoyle horses Robin Hood and Windsor Palace acting as pacemakers for St Nicholas Abbey, and was grateful to Eddie Ahern for doing the same for Frankel on stable-mate Bullet Train.
"I suspected they would go a good gallop, but we had a plan in place. Eddie Ahern did a good job on Bullet Train and it panned out nicely," he said.
Uncertainty remains over how many more outings Cecil will give Frankel, but a career finale at Ascot's British Champions Day in October is a distinct possibility.
Frankel's lucky 13
13 August 2010: European Breeders' Fund Maiden Stakes, Newmarket
10 September 2010: Frank Whittle Partnership Condition Stakes, Doncaster
25 September 2010: Juddmonte Royal Lodge Stakes, Ascot
16 October 2010: Dubai Dewhurst Stakes, Newmarket
16 April 2011: Greenham Stakes, Newbury
30 April 2011: 2000 Guineas, Newmarket
14 June 2011: St James's Palace Stakes, Ascot
17 July 2011: Sussex Stakes, Goodwood
15 October 2011: Queen Elizabeth II Stakes, Ascot
19 May 2012: JLT Lockinge Stakes, Newbury
19 June 2012: Queen Anne Stakes, Ascot
1 August 2012: Sussex Stakes, Goodwood
22 August 2012: Juddmonte International Stakes, York