The decision taken on Wednesday by the 129th IOC Session in Rio de Janeiro underlined the top sports organisation's effort to attract more participation, Xinhua news agency reported.
The IOC session voted unanimously in favour of the sports which were proposed by the 2020 organisers and will make a one-off appearance in the Games.
"Today's (Wednesday) vote was the culmination of a two-year process that began with the unanimous approval of the IOC's strategic roadmap in 2014. The recommendation to give Organising Committees the flexibility to propose new sports for their edition of the Games was intended to put even more focus on innovation, flexibility and youth in the development Olympic programme," said the IOC in a statement.
"We want to take sport to the youth... Tokyo 2020's balanced proposal fulfils all of the goals of the Olympic Agenda 2020 recommendation that allowed it," said IOC President Thomas Bach.
Baseball and softball, which will feature six teams each, will return to the Olympic program for the first time since the Beijing 2008 Games.
Surfing will include 20 competitors in both the men's and women's categories.
Tokyo will host skateboarding, which will comprise two street and two park competitions with 20 male and 20 female participants.
The Nippon Budokan, Japan's martial arts headquarters, will stage karate, expected to be divided into kata and kumite events.
The inclusion of the new sports will add 18 events and 474 athletes while the athlete or event quotas of existing Olympic sports will not be affected.
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