The Eritrean migrant was shot by a security guard in the southern Israeli city of Beersheba.
The security guard mistakenly thought the man was involved in a bus station gun attack in which a soldier was killed and around ten other people were injured.
As the man lay on the ground, bleeding, surrounded by armed paramilitary police, amateur video appears to show him being kicked several times by members of an angry mob.
The Deputy Director General of Soroka Hospital, Jochanan Peiser, says the man suffered multiple injuries.
"The wounded (man) who arrived and was operated on last night suffered gun shots as well as other hard injuries. He sustained multiple injuries in his chest, his lungs and abdomen. We operated on him for hours, but unfortunately we were unable to save him and he passed away."
Police says they're seeking to arrest the people who attacked him.
Spokesman Micky Rosenfeld says video footage will help their investigation.
"An investigation has been opened and we are looking in to see if any civilians damaged him, or caused his death in any way whatsoever, and it's due to the fact that we had CCTV footage of the incident inside the central bus station when the terrorist attack was taking place."
Prime Minister Binyamin Netanyahu has praised citizens who foil attacks, while calling on everyone to abide by the law.
"I would like to send my condolences to the family of the worker from Eritrea. We are in the middle of a long struggle. I think it is obvious that we will win it but this sometimes causes friction between civilians and the centres of the attack. A crowd which stumbles into the scene of an attack should evacuate and allow security and rescue forces to work. We are a law-abiding state. No-one should take the law into their own hands."
A surge in street attacks on Israelis has put the public on heightened alert.
Israel has deployed hundreds of soldiers across the country, and set up roadblocks in Palestinian neighbourhoods of East Jerusalem.
But still Israelis remain fearful.
With parents demanding action to safeguard their children, four Israeli cities have now banned Arab workers from entering schools.
This school security guard says people are no longer trusting.
"People are hysterical and decisions are hysterical. No-one is thinking with logic, everything is scary and fearful. There is no trust in people. It's very sad that this is the situation."
The Knesset party, which represents Israel's Arab minority, has called the move racist.
Israel's Interior Ministry has appealed for municipalities to act with respect and equality towards all their workers, irrespective of religion and ethnicity.
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