Border Reivers fullback Calum MacRae settled the Scots in the fourth minute by slotting his first penalty of the afternoon.
In the first half, England struggled to keep the ball in hand due to the wet conditions, the two wingers squandering a scoring chance each.
On the left, Chris Bell was on his way to the line but when he hit the ground, he lost control of the ball and it popped out of his right arm.
Moments later, this time on the right, Delon Armitage tried to chip the ball into the scoring zone but overcooked it and the five points were thrown away.
Just before the half hour mark, Scotland almost put another five points past the English when Alasdair Strokosch broke the England line and offloaded to Simon Danielli who took the ball at a terrific angle. Craig Hamilton reached the try-line but was denied with only one yard to go.
Dave Walder had the opportunity to level the score on the stroke of half-time but hooked his attempt to the left of the posts.
MacRae's second penalty came in the 53rd minute to put the Scots six points clear of the tournament favourites.
England flyer David Seymore almost put England ahead after 60 minutes when the forwards drove towards the line from a catch-and-drive lineout. The winger crossed the line but was held up.
It took until the 63rd minute for England to put their only points on the board in the form of a penalty try after the referee's patience with the Scotland pack became tired.
The best move of the came only six minutes later when Scotland scored a sublime try. Edinburgh Gunners stand-off Phil Godman gave a beautifully weighted pass to Ross Beattie who forced a hole in the England line. Danielli collected Beattie's offload at pace, cutting a blazing angle to cross the line under the posts. MacRae converted.
In injury time, England threatened to steal the game from the Scots. It took England five minutes of continuous pick and drives to cross the line but eventually, they were held up over the line.
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