Japan kept Scotland at bay for much of the opening period and the hosts could only muster an eight-point lead at the break.
But Murray and his side pushed on in the second-half to secure victory in their first match since the summer.
Mariano Galarza started Argentina's first international of the autumn as the South American nation went head-to-head with England at Twickenham.
The visitors worked hard but couldn't prevent England racking-up four tries to secure a 31-12 victory.
Warriors scrum-half Jeremy Su'a was also in action as he came on as a replacement during Samoa's 40-9 defeat to Ireland.