Kuti announced his disengagement with the statement
"It pains me to say that my spirit has been completely broken and shattered" by last Friday's events, he said.
"It is impossible for me in good faith and in good conscience to get on stage and party and have a good time when so many Africans have lost their lives. Somebody has to mourn them."
Saxophonist and singer Kuti had been set to play on Saturday at the Jazzablanca festival in the Moroccan port city of Casablanca.
But in a video on Instagram, he announced "with great sadness" that he and his band would not be attending.
Jazzablanca confirmed to AFP that Kuti's concert had been cancelled due to "a personal decision by the artist."
Friday's incident was the deadliest in years of attempts by migrants, mostly from southern African countries, to cross the heavily fortified border, one of the EU's only land borders with Africa.
The UN has accused both Moroccan and Spanish authorities of using "excessive force" against migrants, and demanded an investigation.
Spanish media and videos online showed footage of people on the ground, some with bloodied hands and torn clothes.
The June 24 incident was the deadliest in years of attempts by migrants, mostly from southern African countries, to cross the heavily fortified border, one of the EU's only land borders with Africa.
The UN has accused both Moroccan and Spanish authorities of using "excessive force" against migrants, and demanded an investigation.
Despite Kuti's pullout, the show will go on. Ethiopian jazz legend Mulatu Astatke, Brazilian singer-songwriter and politician Gilberto Gil and Israeli folk rock artist Asaf Avidan are still on the concert bill.