Huw Jones scored two tries, with Sean Maitland touching down in between, while Finn Russell delivered a man-of-the-match display to quell doubters that had sprung up in the first two weeks of the championship.
England were well off the pace at a raucous Murrayfield, regularly losing the battle on the ground and suffering from ill-discipline - giving away 13 penalties, one of which saw Sam Underhill sin-binned for a no-arms tackle.
Defeat was just Jones' second as England coach and the Australian offered no excuses for their below-par outing.