A game in front of 70,000 in Texas burst into life in the second half, Daizen Maeda giving Japan the lead but Anthony Elanga levelling minutes later.
Japan, fancied as dark horses in the tournament, were hanging on by the end as Alexander Isak and Elanga both went close.
The Netherlands finished top of a competitive group with seven points, with Japan on five, Sweden four and Tunisia on the plane home with no points.
Graham Potter’s Sweden have also qualified for the knockouts as one of the best third-placed finishers.
The Netherlands, who eased past Tunisia 3-1, will face Morocco in Monterrey while Japan play Brazil in Houston.
Potter, whose side were torn apart by the Netherlands last time out, changed his goalkeeper and started Elanga.
“We had to defend the box and wide areas better,” said the Englishman.
The former Chelsea and West Ham boss added: “The boys were fantastic. Over the course of the game it was a pretty fair result and arguably we were slightly the better team in the second half.”
It remains to be seen who Sweden will play next.
“It’s a tricky one,” said Potter.
“We need to be on our toes in terms of logistics, that’s the fun part of the tournament. (AFP)
