Officers used an armoured vehicle to retrieve the injured victim and take them to hospital, but there was no repeat of widespread destruction of property.
Some two dozen officers in riot gear confronted a group who were throwing rocks and other objects at police near where the black man was fatally shot a day earlier.
Police moved in to try to disperse the crowd and made multiple arrests after skirmishes between protesters and officers on Sunday night.
Local television showed police forming a line and using shields to deflect missiles.
One police officer fell to the ground after apparently being hit by one of the objects and was moved away by fellow officers.
Police also said an injured officer was taken to hospital after a rock broke the windscreen of a squad car.
Earlier, video taken from a media helicopter showed a small group of protesters running through the streets, picking up orange construction barriers and hurling them out of the way.
Police posted on Twitter three locations where they said shots were fired.
There were no other reports of injuries and no major destruction of property after six businesses were burned in the unrest on Saturday.
Police Chief Edward Flynn said at a press conference that the man whose death sparked Saturday night’s rioting was shot after he turned towards an officer with a gun in his hand.
Mr Flynn said the shooting was still under investigation and authorities were awaiting the results of a post-mortem examination, but that, based on the silent video from the unidentified officer’s body camera, he “certainly appeared to be within lawful bounds”.
At the same news conference, Mayor Tom Barrett said a still image pulled from the footage clearly showed a gun in 23-year-old Sylville K Smith’s hand as he fled a traffic stop on Saturday.
“I want our community to know that,” Mr Barrett said. But he also called for understanding for Smith’s family.
“A young man lost his life,” the mayor said.
“And no matter what the circumstances are, his family has to be hurting.”
Mr Flynn declined to identify the officer who shot Smith but said he is black.
After watching the officer’s body camera footage, Mr Flynn said the entire episode took about 25 seconds, from the start of the traffic stop until shots were fired.
He said Smith ran “a few dozen feet” and turned towards the officer while holding a gun.