England, seeking a third Six Nations win 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 to 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.
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, they could not complete the comeback as Scotland claimed their second victory, having agonisingly lost to France last time out.
The South Africa-born van der Merwe became the first Scot to score a hat-trick against England in the Six Nations era.Â
Zooming to 26 tries in his 37th Scotland Test, van der Merwe is only one try 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
With AP