Sule played Takuma Asano onside from a lofted free-kick, leaving defender Nico Schlotterbeck behind the Japanese substitute who raced into the box and fired home from a tight angle for the 83rd minute winner.
Ilkay Gundogan had put the Germans ahead from the penalty spot in the first half but Japan leveled when Ritsu Doan fired home from a rebound in the 75th minute.
“Niklas simply has to pay attention,” Flick told reporters. “He played him onside because he dropped two or three steps too far.
“These are individual mistakes that we had to pay for today.”
Germany had significantly more possession, with 771 passes compared to Japan’s 269, but the Samurai Blue were efficient on the counter.
Kai Havertz had a goal disallowed for offside late in the first half while Japan keeper Shuichi Gonda made some top saves to keep the margin at one goal.
“In the first half we missed a lot of chances,” Flick said. “Japan beat us in terms of efficiency and therefore scored one more goal.
“The individual mistakes that we made must not happen. We knew Japan were quick in transition, and thats what they did today.”