First-half substitute Sofia Huerta tallied in second-half injury time for the only goal for Mexico, which has gone winless in six of its last seven matches at the U-20 Women's World Cup.
The Asian champion controlled from the outset with Hikaru Naomoto hitting the crossbar in the fifth minute. Japan was unable to take advantage of its chances until Hanae Shibata capitalized on a goalmouth scramble and poor clearance by Cecilia Santiago, hitting a shot that deflected in the 32nd minute.
Tanya Samarzich had two of Mexico's best efforts in the 38th and 51st minutes, but Japan began to exploit its 24-8 advantage in shots in the second half, doubling its lead in the 56th when Naomoto converted a right-footed effort from distance.
Kumi Yokoyama added another shot from distance in the 77th and Yoko Tanaka tacked on a penalty 12 minutes later before Huerta replied for Mexico in the first minute of injury time.
Mexico on Wednesday next faces Switzerland, which has lost all seven games in the U-20 Women's World Cup, including a 2-1 defeat to New Zealand earlier Sunday.