In a video released online, IS claimed it had killed the 47-year-old journalist - the second purported beheading of a Japanese hostage in a week - but made no mention of a Jordanian pilot it had also threatened to kill.
Japan has said it was "highly probable" that the video was authentic.
Mr Goto, 47, had devoted his life to giving a voice to victims, particularly children in conflict zones.
As the country mourned, some 200 people rallied outside the office of prime minister Shinzo Abe, who condemned the killing as "heinous and despicable".
In a show of defiance after the killing, Mr Abe vowed to increase Japan's humanitarian aid for countries fighting IS militants.
"We will never forgive terrorists," Mr Abe said, appearing to fight back tears as he spoke.
"The government has been working with the utmost efforts on the issue - I deeply regret that this is the result."
Mr Abe said Japan would never give in to terrorists and would continue to work with international partners to bring them to justice.
"We will cooperate with the international community to make them atone for their crimes," he said.
Mr Goto's mother, Junko Ishido, who earlier appealed for his safe release, appeared before the media in Tokyo after the video was released.
She tearfully pledged to continue her son's efforts towards making "the world a place without any wars, and to save children from war and poverty".
"I promise here to carry out his legacy, hopefully with your support," she told reporters at her home.
"I hope Kenji's death ... [will] contribute to the world however small it may be."
source : ABC
Monday
2 February 2015
6:05:28 AM
668688
Hundreds of people have gathered outside the Japanese prime minister's office in Tokyo to hold a silent vigil in honour of journalist Kenji Goto, who was executed by Islamic State militants.