Protesters flocked to rallies in Istanbul, Ankara and Izmir to call for an end to discrimination after two men were caught up in clashes between police and protesters in a predominantly Alevi district on Thursday and killed.
Turkey has launched an investigation into the deaths of the two men, who were not among the demonstrators.
The Alevi community follows a moderate form of Islam and makes up around a quarter of Turkey's 76 million citizens.
"We warn the government: Get your hands off Alevis."
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Several hundred protesters, including lawmakers, musicians and actors, shouted "murderer state will be held accountable," as they marched through the streets of Istanbul.
Ugur Kurt, 30, died from gunshot wounds to the head during an Alevi funeral while Ayhan Yilmaz, 42, was hit by a hand grenade during clashes.
The deaths came with tensions high ahead of the first anniversary of deadly anti-government protests and in the wake of a mine disaster that claimed 301 lives last week.
Erdogan today extended his condolences to both victims, days after he branded the demonstrators "terrorists" and defended the actions of police who used tear gas and fired live rounds into the air.
The Alevis have been strong supporters of Turkey's secular system, but the state has never recognised their faith, perpetuating discrimination against a group that makes up about a quarter of the Sunni-majority country's population of 76 million.
They were also angered by a package of social reforms last October that offered new freedoms to the Kurdish minority but failed to address Alevi demands for the recognition of their places of worship.