Two well-struck goals from free kicks by Keisuke Honda, after 17 minutes, and Yasuhito Endo on 30 minutes, gave Japan a 2-0 halftime lead.
Denmark pulled back a goal nine minutes from time when Japanese keeper Eiji Kawashima saved a Jon Dahl Tomasson penalty but the Danish forward scored from the rebound. Japan scored a late third through Shinji Okazaki three minutes from time.
Japan became the second Asian team after South Korea to qualify for last 16. They meet Paraguay in Pretoria on June 29.
On a cold night at the Royal Bafokeng Stadium, Japan took control from the start and, though they conceded possession readily, stretched the Danish defense with ease.
Their intricate, almost meticulous, one-touch play and the speed of their movement created a series of chances, Daisuke Matsui stretching to meet an angled cross by Yoshito Okubo that hit the diving Danish keeper Thomas Sorensen's right knee from just one of many.
If that was a warning for Denmark, it was not heeded and Japan, enjoying midfield superiority, duly took the lead after 17 minutes with a superb goal by Honda. Taking a free-kick 30 meters out on the right, he struck a left-foot shot that faded to the left and left the flat-footed Sorensen helpless.
Denmark tried to exploit their height advantage - a ploy the Japanese blunted with excellent marking and brave defensive play.
Jon Dahl Tomasson shot narrowly wide and had another effort saved, but the Danes were left reeling when Per Kroldrup tripped Okubo and Endo curled a right-foot free-kick round a defensive wall and inside Sorensen's left post from 25 meters.
Japan sat back to absorb a Danes' late onslaught in which Tomasson pulled one back before the Asian side ensured their progress to the next stage through Okazaki late goal.
