England, seeking a third Six Nations win of their own for the first time since 2020, led through a George Furbank try after five minutes and looked in control, only for Van der Merwe to strike twice and help the hosts to a somewhat flattering 17-13 halftime lead in Saturday's fixture in Edinburgh.
The winger, who scored two superb tries in Scotland's victory at Twickenham last season, collected a Finn Russell kick three minutes into the second half for his third, and two Russell penalties stretched Scotland's lead to 30-16.
"I can't believe it to be honest, but I have to thank the boys for giving me the opportunity," Van der Merwe said after his side lifted the Calcutta Cup.
"We had a really good first phase, there was a lot of space open and I knew Finn was going to kick it to me. Lucky for me it bounced in my hands."
Scotland's Duhan van der Merwe flies in for one of his three tries against England. (AP PHOTO)
England emptied their bench and replacement wing Immanuel Feyi-Waboso grabbed their second try after 66 minutes.
But, unlike in their opening wins over Italy and Wales, the English could not complete the comeback as Scotland claimed their second victory of this year's championship, having agonisingly lost to France last time out.
"You have to celebrate these moments, especially when you have a trophy in the dressing-room," Scotland coach Gregor Townsend, who has overseen five wins and a draw in the last seven Calcutta Cup matches, said.
"Duhan was great today. He saw the opportunities and went for it.
"The first try was really special in that we didn't have much ball, we weren't in England's half very often."
The South Africa-born Van der Merwe became the first Scot to score a hat-trick against England in the Six Nations era.
Zooming to 26 tries in his 37th Scotland Test, Van der Merwe is only one behind the Scotland record held by Stuart Hogg, who retired last year.
He finished the match in the sin bin, but received huge applause walking off after he was yellow-carded in the 79th minute for a dangerous tackle.
Van der Merwe's finishing was complemented by captain Russell off the tee. He went six for six at the posts, and he's perfect in the tournament with 15 out of 15.
George Ford tried to keep England close with 11 points, including a 35-metre drop goal.
England coach Steve Borthwick relied on his regular line that his team were still learning.
"We have to give credit to Scotland, it was a very strong performance," he said.
"You saw a Scotland team that have been together a good number of years and are clear what they are trying to do against an England team that are tying to develop."
- with AP
