The unrest erupted after a policeman allegedly killed the man and wounded two others during an argument over the price of a cup of tea.
The policeman has been arrested and the case referred to prosecutors.
Video footage showed angry protesters overturning a police vehicle while chanting "the police are thugs".
Egypt has seen a series of allegations of police brutality in recent months, stoking public anger.
The interior ministry said that Tuesday's incident in the eastern suburb of Rehab began with an argument over the price of a cup of tea between several policeman and a street vendor.
One policeman opened fire, killing the vendor and wounding two passersby, it added.
Photographs showed what appeared to be a man lying still on the floor, covered in blood, surrounded by angry onlookers.
Witnesses said the protest began shortly after the incident.
"Security forces brought in two riot police vehicles and an armoured truck and the victim's family is here and pelting them with rocks," one witness told the Reuters news agency.
"Security forces are retreating and promising justice but the crowd is demanding police hand over the killer."
In February, there was a protest outside the Cairo security directorate after a policeman reportedly shot dead a driver in a street in an argument over a fare.
There were also riots in Ismailia and the southern city of Luxor after at least three people died in police custody in a single week in November.
The government has also been forced to repeatedly deny allegations that security services were responsible for the killing of Italian academic Giulio Regeni in Cairo earlier this year.
Officials have blamed a criminal gang for his abduction and torture.

The skeleton of "Thankerton Man" was found in a stone cist - a type of burial chamber - at Boatbridge Quarry, Thankerton, South Lanarkshire, in 1970.
It was radiocarbon-dated to between 2460BC and 2140BC and thought to have been that of a man aged 18 to 25.
The reconstructed image will go on show at the Biggar and Upper Clydesdale Museum, which opens on Tuesday.
The reconstruction was produced by specialists from Dundee University's Centre for Anatomy and Human Identification (CAHID) who worked from detailed analysis of the skull.
Caroline Erolin, lecturer in forensic and medical art at CAHID, said: "Given its age, the skeleton of Thankerton Man was in excellent condition, which allowed us to get a strong impression of how he may have looked.
"Once we built the basic shape of his face we then looked at historical data to get a better idea of how a man would have looked at that time. For instance, we know they had the ability to shave."
The estimated height of the man was around 1.8 metres (5ft 11ins), which is regarded as tall in Copper Age terms.
The cist contained a finely-decorated beaker which had held food or drink for the deceased's journey into the afterlife.
The pot and skeleton are curated by National Museums Scotland.
Dr Alison Sheridan, principal curator of early prehistory at National Museums Scotland, who provided archaeological advice, praised the reconstruction.
She said: "This is a magnificent piece of work that really brings the past to light. It has spurred us on to arrange the DNA analysis of this man's remains."

It is the first time that a non-premium brand has come first in the annual study by consultancy J.D. Power.
The survey of more than 80,000 car buyers found that Kia had the fewest problems in the first 90 days, followed by Porsche, Hyundai, Toyota and BMW.
Worst performers were Daimler's Smart, Fiat, Volvo, Land Rover and Mini.
In the ranking of 33 cars brands, 21 saw an improvement over the past year.
The study also showed that for only the second time in the past 30 years, US brands received better marks collectively than foreign cars.
J.D. Power said that in past years, electronic features such as Bluetooth, voice recognition and touch screens had often been prone to glitches dragging down the results and that this year carmakers had managed to improve their reliability.
Together with its affiliate Hyundai Motor, Kia is the world's fifth largest automaker by sales.
Hundreds of people have taken to the streets of Egypt's capital, Cairo, to protest after a tea vendor was allegedly shot dead by police.
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Scientists from Dundee University have recreated the face of a young man who lived more than 4,000 years ago.
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South Korean car maker Kia has come top in a closely watched US car quality ranking, edging out the luxury brands that usually claim the crown.