Later in the day, group rivals Senegal beat Poland, 2-1.
The Lions of Taranga played with tremendous confidence which eventually paid off with a first half goal.
With Japan dominating in midfield, Colombia's Argentine coach Jose Pekerman opted to sacrifice Juan Cuadrado around the half hour mark to send on defensive midfielder Wilmar Barrios.
Poland missed key defender Kamil Glik against Senegal but the bulky Monaco center-back is expected to start his World Cup campaign against Colombia.
Reports of attempt on Zimbabwean President Emmerson Mnangagwa’s life
An explosion has rocked a stadium in Zimbabwe where the nation's President Emmerson Mnangagwa was addressing a rally on Saturday. Bulawayo has always been a bastion of opposition to the ZANU-PF and it was Mnangagwa's first rally in the city.
Colombia defeated Japan 4-1 when the teams met in group play in Brazil four years ago, and the Japanese also began the game without Shinji Okazaki, a Leicester forward who has been trying to overcome a sore calf.
Japan became the first-ever team from Asia to defeat a Southern American squad in a World Cup game, after three draws and 14 defeats.
"We made enough prep work before the game and it worked well".
She arrived Monday in Russian Federation and will stay through June 26, and is expected to attend Japan's next two group stage matches against Senegal and Poland.
Game of Thrones co-stars Kit Harington, Rose Leslie to Wednesday
But numerous actors and actress reunited today to witness GOT stars Kit Harington and Rose Leslie , both 31, get married. Kit , who plays Jon Snow on Game Of Thrones , is marrying his co-star Rose Leslie in Scotland today (23 June).
"It was tough right until the end but everyone fought to defend the lead and we were able to get the right result", goalkeeper Eiji Kawashima said. "We need to be strong, have character and show the power of our team".
Being the Honorary Patron of the Japan Football Association, Princess Takamado has attended all FIFA World Cups since 1998.
They took the lead shortly before half-time after an Idrissa Gueye shot was deflected off Thiago Cionek.
Cissé, who captained the Senegalese side that created wonders at the 2002 World Cup, knows the importance of discipline in tournaments such as the World Cup.
Hundreds of separated migrant families reunited
The father told the AP in a phone interview that he spoke to his son once by phone since they were separated 26 days earlier. Trump signed an order Wednesday to end the practice, which was part of his administration's " zero tolerance " policy.
Japanese and Senegalese supporters received praise after they were seen picking up their trash and tidying up their stadium section following their respective matches Tuesday. This could be one of those matches where both teams park the bus and are fine taking a point to increase the odds of advancing to the next round.