Michael Brown died Saturday in the St Louis suburb of Ferguson, Missouri, sparking unrest and allegations of police racism.
Witnesses and law enforcement have given conflicting versions of how the 18-year-old was shot dead in broad daylight, just two days before he was due to start college.
"Now is the time for peace and calm on the streets of Ferguson," Obama told reporters. "Now is the time for an open and transparent process to see that justice is done."
Television and social media footage showed thick clouds of smoke and protesters scurrying through it. In one sequence, police fire gas at a TV news crew then dismantle its abandoned equipment.
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Police also used sound bombs and rubber bullets to disperse crowds.
Noting the raw emotions, Obama said local authorities had a responsibility to be "open and transparent" about how they were investigating Brown's death and protecting the community.
"There is never an excuse for violence against police or for those who would use this tragedy as a cover for vandalism or looting," he said.
Amid yesterday's tension, police also arrested, and later released without charge, two journalists covering the events.
Wesley Lowery, a Washington Post political reporter, and Ryan Reilly, who works for the Huffington Post, were detained in a McDonald's after police entered the eatery and ordered people to leave, the pair wrote on Twitter.
Obama referenced the incident, warning: "Here in the United States of America, police should not be bullying or arresting journalists who were just trying to do their jobs and report to the American people on what they see on the ground."