Habtom Zarhum, 29, was shot by a security guard this week at a bus station in the southern city of Beersheba after being mistaken for an assailant in an attack that killed an Israeli soldier.
He later died of his injuries.
Footage of Zarhum bleeding as an angry mob rains blows on his head and torso has spread rapidly on social media, prompting soul searching among Israelis over their response to a wave of attacks as well as their treatment of African migrants.
One photo posted on Facebook shows Zarhum smiling with colleagues at a nursery where he worked.
Neta Singer, who worked with Zarhum, remembered how he liked to sing and dance, and how he would send his entire monthly salary back to his family.
He never complained, she said.
"If I could ask him to forgive all the evil that was done to him, I know he would forgive it," Singer insisted, adding the traditional Jewish eulogy: "May his memory be a blessing."
Zarhum's autopsy ruled he died of gunshot wounds, rather than the vicious beating he received from bystanders as police officers looked on.
His death comes in the middle of a surge of violent attacks across Israel and the occupied West Bank that has seen at least 47 Palestinians killed, often after knife attacks targeting Jews.
Eight Israelis have also died, and the attacks have put intense pressure on Israeli Prime Minister Benjamin Netanyahu to stem the violence.
Following Zarhum's death, Netanyahu publicly called on Israelis not to take justice into their own hands, but many see the young man's killing as part of a wider problem in Israel's treatment of African asylum seekers.
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"This man was killed because he was black and because he was mistaken for a terrorist (even though) he was wearing flip-flops and holding his visa," Emanuel Yamami, a member of Tel Aviv's Eritrean community, told AFP.
"He was shot like an animal, and then beaten. The police were there and they did nothing to stop it."
Sari Bashi, the Israel/Palestine director at Human Rights Watch, called the death a "tragic but foreseeable outgrowth of a climate in which some Israeli politicians encourage citizens to take the law into their own hands".
Official figures show 45,000 illegal immigrants are in Israel, almost all from Eritrea and Sudan. African communities complain of marginalisation, and they have held several protests this year against their alleged mistreatment.
The UN says as many as 53,000 refugees have crossed Israel's southern border with Egypt, including 36,000 from Eritrea.
Many are fleeing persecution and they head to Israel due to its high standard of living and its relative ease of access over land from Africa.
Those close to Zarhum say he once served as a pilot in Eritrea's air force before fleeing his homeland's dictatorship to Sudan.
He arrived in Israel four years ago, finding work at a nursery in the Ein Habesor kibbutz in southern Israel's desert Negev region, where he lived.
On Monday evening, migrants at the Holot detention centre held a vigil in Zarhum's memory. There are plans to hold a similar event on Wednesday evening in Tel Aviv, which has a large African minority.
Eritrea's ambassador to Israel, which has been strongly condemned by rights groups for its treatment of African migrants, has called for an enquiry into Zarhum's death.
"We are in contact with relatives," the embassy told AFP, adding that his body will be "repatriated to Eritrea after the Israeli police release it".