The horse, reckoned by many to be the finest and fastest ever seen, eased through on the inside and coasted home by seven lengths in the one mile, two furlongs race.
The win was his eighth in a row at Group One level.
Sir Henry Cecil, who has been receiving treatment for cancer, was in attendance to see the horse he trained prove his dominance once again.
It is almost certainly the penultimate race of Frankel's career, and despite the new distance he went into the race a 1/10 favourite in an illustrious field.
Farhh took second place, while St Nicholas Abbey finished third.
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.
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.
"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.
"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.
A potential career finale at Ascot's British Champions Day in October is much anticipated, but as yet uncertain.