The Brave Blossoms produced arguably the biggest shock in World Cup history by beating two-time champions South Africa on the opening Saturday of the tournament, a result that saw them leapfrog Scotland in the world rankings.
They had just four days before taking on Scotland at Kingsholm Stadium, and fatigue appeared to play a part as Vern Cotter's side ran in five unanswered second-half tries to claim a bonus-point victory.
Despite that, Jones refused to make any excuses for his side's performance after the break, insisting that they were simply outplayed.
"I said we weren't going to use it as an excuse and we're not," the Australian-born coach, who will leave his role at the end of the tournament, told Sports Mole.
"Scotland we're too good for us. They played too well in the second half. They scored 33 points in the second half to our [three]. We're not using that as an excuse."
Japan trailed by just two points in the early stages of the second half before Scotland took the game beyond their opponents.