Jose Pekerman's side, so impressive in securing wins over Greece and Ivory Coast earlier in the tournament, were already assured of qualification and knew a draw would be enough to secure their passage as group winners.
Japan, meanwhile, needed to win and hope the result between Ivory Coast and Greece went their way in order to progress.
The South Americans hit the front shortly after the quarter-hour mark, Juan Cuadrado smashing home a penalty after Yasuyuki Konno had fouled Adrian Ramos.
Japan equalised on the stroke of half-time, Shinji Okazaki squeezing a header inside the near post to raise hopes of qualifying.
Yet Colombia then pulled clear in the second half, Jackson Martinez scoring twice following assists from half-time substitute James Rodriguez, who added a delightful late fourth.
Colombia will now take on Uruguay in the second round, while Japan exit the tournament having finished bottom of their group.
Japan made the stronger start as Colombia struggled to find their feet having made eight changes from their victory over Ivory Coast.
However, it was the South Americans who went in front after 17 minutes, following their first real foray forward.
Konno needlessly brought down Ramos inside the area, and Cuadrado dispatched the spot-kick, prompting further choreographed celebrations from the Colombians.
Japan responded well, Shinji Kagawa creating space on the edge of the box before firing in a low shot which was tipped behind by David Ospina.
Keisuke Honda was the next man to go close, sending a dipping free-kick narrowly wide of the right-hand post in the 33rd minute.
Colombia ought to have doubled their lead three minutes before the interval, Martinez firing wide of the target from 14 yards after being picked out by Ramos.
They were made to rue that miss soon afterwards, Okazaki flicking home Honda's right-wing cross with the final touch of the half.
Half-time substitute Carlos Carbonero wasted a golden chance to restore Colombia's advantage in the 54th minute, stabbing the ball over the crossbar after a devilish ball in from fellow replacement Rodriguez.
It mattered little as Martinez made it 2-1 a minute later, taking a touch and firing low beyond Eiji Kawashima after a nicely-weighted pass from Rodriguez inside the area.
Eder Alvarez Balanta was perhaps lucky to escape punishment after his forearm struck the face of Okazaki in the corner, drawing blood from the nose of the Japan goalscorer.
Honda continued to pose a threat from set-pieces, bringing a save out of Ospina with a rasping free-kick in the 64th minute.
Yoshito Okubo went close a minute later, meeting Atsuto Uchida's low cross at pace only to see his close-range effort fly over the bar.
Martinez doubled his tally eight minutes from time with a cool finish, and moments later Kagawa summed up a disappointing campaign for the Japanese by firing wide with just Ospina to beat from close range.
There was a notable moment five minutes before the end, as 43-year-old goalkeeper Faryd Mondragon - retiring after the tournament - was brought on in place of Ospina to become the oldest player in World Cup history.
Rodriguez, one of the players of the tournament so far, showed his class in the 90th minute to round off the scoring, turning Maya Yoshida inside out and dinking an impudent finish over Kawashima, before Mondragon made an injury-time save to deny Yoichiro Kakitani.
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