The Blue Samurai were two goals up by the half-hour mark as they cruised into the knockout stages on foreign soil for the first time in their history, where they will face Paraguay on Tuesday for a place in the last eight.
Man-of-the-match Honda broke the deadlock in spectacular style after 17 minutes, firing a 30-yard free-kick over a three-man wall into the far corner past Thomas Sorensen on a night to forget for the leaden-footed goalkeeper.
If the Stoke stopper was partly at fault for Honda's opener, there was little he could do when, 13 minutes later, Endo stepped up to curl home right-footed from a similar distance, if anything an even better strike than the first.
With his confidence seemingly in tatters, Sorensen was then saved by the woodwork as he spilled a routine Endo free-kick after the break as the free-flowing Japanese threatened to run riot.
Only after the break when they threw men forward in a desperate attempt to secure the win they needed to progress did Denmark cause problems for the Blue Samurai as substitute Soren Larsen struck the bar from long range.
Former Newcastle forward Jon Dahl Tomasson pulled a goal back with nine minutes left, but it was too little, too late and failed to set up a grandstand finish.
The veteran striker ended a two-and-a-half year wait for an international goal to set a new Danish record with the 52nd of his career as he followed up to chip home the rebound when Eiji Kawashima saved his penalty following skipper Makoto Hasebe's foul on Daniel Agger.
There was still time for more magic from the unselfish Honda, whose stunning turn and pass in the box put the third on a plate for substitute Shinji Okazaki three minutes from time to round-off a thoroughly deserved victory.
Denmark (4-3-3): Sorensen, Jacobsen, Agger, Kroldrup (Larsen 56), S Poulsen, Jorgensen (J Poulsen 33), C Poulsen, Kahlenberg (Eriksen 63); Tomasson, Bendtner, Rommedahl.
Subs (not used): Andersen, Gronjkaer, Christiansen, Mtiliga, Kvist, Jensen, Enevoldsen, Beckmann.
Japan (4-5-1): Kawashima; Komano, Nakazawa, Tanaka, Nagatomo; Hasebe, Matsui (Okazaki 74), Abe, Endo (Inamoto 90), Okubo; Honda.
Subs (not used): Narazaki, Kawaguchi, Uchida, Iwamasa, Konno, S Nakamura, K Nakamura, Tamada, Yano, Morimoto.