On February 26, 2010, Seba was involved in a traffic collision upon exiting the Shuto Expressway at 22:14. He was pronounced dead at a hospital in Shibuya Ward after efforts to revive him failed. His grave is located within the Japanese section of Tama Cemetery.

Seba's death has elicited many tributes from other artists around the world. On Bandcamp, the New York-based Digi Crates records have released a series of tribute albums performed by various artists in a style reminiscent of Seba's. In addition, Seba's label Hydeout Productions released a tribute album titled Modal Soul Classics II featuring a number of former collaborators and with lyrics and song titles referencing select tracks from both Modal Soul and Metaphorical Music, such as the track "Music is Ours", which directly references "Music is Mine", the 5th track of Modal Soul.

Frequent collaborator Shing02 has performed at many tribute concerts for Seba, and has remarked that "Through his soulful music, Nujabes has touched so many people around the world, even beyond his dreams", and "[I] deeply regret the loss of a unique talent and a close friend."

In 2013, Australian producer Ta-ku released the Tribute "25 Nights for Nujabes".

Daniel Hodgman, founder of hip hop culture website BonusCut, in a 2014 highlight of Modal Soul said that, "Nujabes may not be physically with us anymore, but through his music, his legacy and lust for life lives on." Co-founder Gus Navarro remarked that, "The music of the late producer Nujabes is something to hold onto and never let go."

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