The shooting at the Six Stars Market was just four miles from the suburb of Ferguson, which has been rocked by racially-charged riots after a white officer killed unarmed black teenager Michael Brown 11 days ago.
The violence has raised questions about the state of US race relations nearly six years after Americans elected their first black president, Barack Obama.
In the latest incident, the suspect was said to be armed with a knife and charged at officers.
The 23-year-old stole two energy drinks, according to reports, before returning to take a pastry and becoming involved in an argument with the owner.
The officers left their patrol car without their weapons drawn but when the man charged at them with the knife raised and was within three or four feet, they opened fire and killed him at around 12:30pm local time (6:30pm GMT).
Police Chief Sam Dotson waded into a large crowd which gathered at the scene in an apparent effort to calm tensions. Many chanted “hands up, don’t shoot”, which was heard in Ferguson following the shooting 11 days ago of 18-year-old Mr Brown.
In nearby Ferguson, there was a temporary calm yesterday which followed police coming under heavy gunfire on Monday night. They arrested 31 people. This was despite the deployment of National Guard troops and the lifting of a curfew to allow protesters to have more freedom to demonstrate.
“We over-policed for a few days, and then we completely under-policed,” said senator Claire McCaskill, a Missouri Democrat. She said she was working with local leaders on ways to quell the violence.
Possible methods include screening for weapons and moving protest areas away from the business district to open green spaces. Both she and US Representative Emanuel Cleaver, another Democrat, said calm was needed to allow federal investigators to evaluate the evidence.
“What’s happening now is damaging, or interfering, with what needs to be done,” Mr Cleaver said.
On Monday, Mr Obama said he told Missouri governor Jay Nixon use of the National Guard should be limited, and he also called for conciliation. Attorney general Eric Holder plans to visit Ferguson today to reassure that justice will run its course.
Ferguson, a community of roughly 21,000 mostly black residents just outside St Louis, has a long history of racial tension. Blacks have complained of police harassment and under-
representation in city leadership. Tension boiled over 11 days ago after Mr Brown was shot dead while walking down a residential street on the afternoon of 9 August. City police refused to immediately release the name of the officer who killed him. They later identified him as Darren Wilson, 28, but still have not provided details about why he fired multiple rounds.
Since the killing, thousands of protesters have taken over the site of the shooting and the nearby business district each night, chanting anti-police slogans and carrying signs calling for Mr Wilson’s arrest.
Police also closed a road to traffic to provide a path for marchers. But police said some in the crowd hurled bottles, rocks and petrol bombs at officers, who responded by firing gas-filled canisters and a noise cannon to disperse the throng.
State Highway Patrol Captain Ron Johnson, who is overseeing security in Ferguson, said officers had come under “heavy gunfire”, but did not return it.
Riot police did confiscate two guns and what looked like a petrol bomb from protesters. Four officers were injured, he said.