Yoko Tanaka scored with free kicks in each half, and Asuka Nishikawa and Hikaru Naomoto added second-half goals as Japan improved to seven points from two wins and a draw in group play.
Tanaka opened the scoring at National Stadium with a 20-meter free kick in the 30th minute and doubled the advantage three minutes after the break with another curling free kick from the same distance.
"We have some momentum going into the next round," said Tanaka, who had four goals in the group stage. "It's Japan against South Korea so you know it will be exciting. We're only thinking of winning it all."
Nishikawa made it 3-0 in the 52nd minute and Naomoto sealed the win in the 84th minute on a penalty kick after being taken down in front of the goal by Swiss goalkeeper Nadine Boeni.
Japan will play South Korea in the quarterfinals, which begin on Thursday.
Four goals in the second half from Sofia Huerta, Natalia Gomez Junco, Yamile Franco and Olivia Jimenez saw Mexico books its place in the next round where it will face Nigeria.
Elsewhere, Jeoun Eun-ha scored twice late in the second half as South Korea also advanced to the next round with a 2-0 win over Brazil in Group B.
Francisca Ordega scored a hat trick as Nigeria coasted to a 4-0 win over Italy in Group B's other game to advance.
Defending champion Germany was the first team to book its place in the quarterfinals.