Phil Foden and Harry Kane were also on target as the Three Lions tamed the roar of Hampden Park and Scotland's five-game winning streak on Tuesday.
Manager Didier Deschamps made six changes from their last outing, a 2-0 win over Ireland, including benching star striker Kylian Mbappe.
Japan, who also contributed to Germany's group stage exit at the World Cup with a 2-1 win in Qatar last year, scored twice in each half
Only 10 of the 23-man squad that took Brazil to a disappointing quarter-final exit at the World Cup made the trip to Morocco for the game.
