For the crestfallen Wallabies, it was the first time they had been swept in a three-Test series at home since 1971 when South Africa completed the feat.
England played with more enterprise than in the second Test in Melbourne, but they also secured a bigger share of possession than in that game.
The match ebbed and flowed with six lead changes, but England's late surge again underlined the ability to finish strongly.
While previous northern-hemisphere sides touring Australia have flagged after a tough domestic campaign, Jones' England have kept going to the end.
Farrell, five-eighth George Ford and halfback Ben Youngs pulled the strings in the backs, while the hard-running Vunipola brothers, prop Mako and No.8 Billy, led the charge for the visiting forwards.
Australia produced some sparkling passages of play, but lacked discipline, allowing sharpshooter Farrell too many shots.
Fullback Israel Folau and back-rowers Michael Hooper and Sean McMahon spearheaded the Australian effort, with the Wallabies showing much more creativity than in their flat second Test performance.
England started in enterprising fashion, with Dan Cole crossing following good work from fellow prop Vunipola.
Australia responded well with tries to five-eighth Bernard Foley and winger Dane Haylett-Petty, his first at Test level.
Folau was instrumental in setting up both five-pointers.
Fullback Mike Brown burrowed over as England regained the lead, only for a Foley penalty on the bell to give the Wallabies a one-point lead at halftime.
Australia lost lock Rob Simmons with an AC injury and he was replaced by debutant Adam Coleman at halftime.
The see-saw nature of the game continued after the break, with Billy Vunipola crossing from the back of a scrum to grab the lead back for the visitors.
Tries to Hooper and Folau set up a 32-28 lead for the Wallabies, but two Farrell penalties and a conversion of a try to reserve hooker Jamie Cole regained the advantage for England which they never surrendered.
A late try to substitute winger Taqele Naiyaravoro was scant consolation for Australia.