The victory completed a stunning Asian hat-trick for Murray and allowed the seemingly unstoppable Scot to leapfrog 16-times grand-slam champion Federer into third spot in the ATP list.
Murray’s 25th victory from 26 matches sends Federer out of the top three for the first time in eight years.
Murray has now won three titles in as many weeks on the Asian swing of the ATP World Tour – his best winning streak – after his victories in Bangkok and Tokyo.
“If you finish in front of Federer in a year, then there’s not many people in the last five, six, seven years that have been able to say that,” said Murray.
“I’m still not guaranteed to finish (the year) at number three; I’m still going to have to win some more matches,” the Scot added.
“This is the best tournament run of my life. I was very nervous as I wanted to retain the title.”
The defending champion broke the third-seeded Ferrer in the first game but a catalogue of errors then undermined his hard work.
Spaniard Ferrer, hoping for revenge for his 6-2 6-3 semi-final loss to Murray last weekend, double-faulted with the first set poised at 5-5.
Murray leaped on the error and produced a pair of aces to secure the set.
World number five Ferrer was seeking his first Masters title but his hopes were dashed by an increasingly dominant Murray who ran him ragged for much of the second set.
The Briton lobbed to break Ferrer at 1-1, broke again to repel the Spaniard’s last-ditch rally and finished off the match with a sizzling forehand.
“It is difficult to beat Andy at the moment; he is playing very confidently,” said Ferrer. “Maybe in the first set I had my chance at 5-5 30-30 but I played so bad in that game. After that, I served badly for a very long time.”