The Iranian artist Shirin Neshat, whose work focuses on the inner life and struggles of Muslim women, was also among the big winners of the Praemium Imperiale, the lucrative annual awards of the private Japan Art Association.
But overall it was African artists who dominated, with the Ghanaian sculptor El Anatsui also receiving one of the top prizes, worth 15-million yen (USD 136,000, 117,000-euro) alongside the Spanish architect Rafael Moneo.
Every year since 1989, the Praemium Imperiale has been awarded in five different disciplines -- music, painting, sculpture, architecture and theatre/film.
N'Dour, 57, a sometime politician as well as what Rolling Stone magazine dubbed the "most famous singer in Africa", is best known for "7 Seconds", his hit song with Neneh Cherry.
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He is also seen as an ambassador for peace and religious tolerance.
Anatsui, 73, who is based in Nigeria, is the first Ghanaian to win the prize.
He is best known for reusing thrown-away everyday objects in his often dazzlingly beautiful mosaics, and was awarded the Golden Lion at the Venice Biennale in 2015 for his life's work.
Previous recipients of the prize include painters Jasper Johns and Willem de Kooning, architects Frank Gehry and I.M. Pei, film-makers Federico Fellini and Akira Kurosawa, playwright Arthur Miller and Indian sitarist Ravi Shankar.
The awards were created in 1988 in honour of the late Japanese Prince Takamatsu, who served as honorary patron of the private association for 58 years until his death in 1987.
The prizes will be awarded at a ceremony in Tokyo on October 18.