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.
"We knew the significance of the game," Jones said.
"We knew what we would get thrown at us at Murrayfield - 65,000 people all passionate about Scotland. You get off the bus and people are yelling abuse at you.
All the key moments from a classic #SCOvENG encounter in three minutes
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"We knew all of that but we weren't good enough to handle it. You have got to be good enough to handle it and we weren't today. I apologise for our performance.
"They beat us at the breakdown, we did not get a defensive spacing right in the first half and they were able to cut holes in us. That's disappointing.
"I have got take responsibility for the performance because we weren't there. I take full responsibility and I have to work out what I did wrong and work out how to fix it."
Reports emerged just before kick-off that star back Owen Farrell had been involved in a fracas with members of Scotland's squad.
The Saracens man appeared unfazed, scoring a try and enjoying a 100 per cent success rate with the boot, and Jones did not believe it contributed to a defeat he is determined to learn from.
"I don't know about it," Jones said of the alleged skirmish. "If there was, we shouldn't let that detract from a great Scotland victory.
"Any time we got momentum, they were able to turn us over or get a penalty, which stifled our attacking game. They contested really well and read the referee superbly and got the reward for it.
"These lessons you don't want to have but they are the best lessons in the world. We will learn a lot from this. Unfortunately, the lesson isn't sometimes nice to take but it is a great lesson for us."
Photo Getty Images. Caption: Huw Jones scores for Scotland