The protests were a show of solidarity with the BLM movement and African American George Floyd, who died while being arrested in Minneapolis, 9News reported.
Protesters in Australia were also aiming to support the Aboriginal community and highlight high levels of indigenous incarceration and deaths in custody.
Thousands of people gathered on the steps of Sydney's Town Hall, chanting "Black Lives Matter".
Other chants of "no justice, no peace" and "no racist, police" were heard.
Rally organizers in Sydney urged protesters to wear masks and move in groups of ten around Sydney's Town Hall Square.
"We don't want to get sick," the organizers told the crowd.
NSW's Court of Appeal has rejected the decision to ban the rally in Sydney, making today's demonstration officially legal.
It comes after the highest court in NSW banned the Sydney protest because it breached coronavirus restrictions, but the warning failed to stop the marches.
More than 10,000 Victorians also gathered at the Black Lives Matter protest in Melbourne's CBD today despite orders to stay home due to the coronavirus pandemic.
People were masked but refused to be silenced, as crowds funneled together down Bourke Street.
Clapping and chanting also erupted as crowds surrounded the steps of State Parliament, with people holding signs including "Black Lives Matter", "No Room for Racism" and "White Silence Is White Violence".
A traditional didgeridoo and smoking ceremony also took place outside Flinders Street Station.
A sea of Aboriginal flags also flooded streets, with speeches expressing the death in police custody in the US was no different to what Aboriginal people have experienced in Australia.
Speakers remembered more than 430 Indigenous people lost in police custody.
Thousands of people have also flocked to inner-city Brisbane to protest police brutality against indigenous Australians and call for justice for those who have died in custody.
Crowds spilled from King George Square to neighboring blocks, with people packing stairwells and balconies to get a view while others brandished signs calling for reform in Queensland and across the globe.
Speakers, including elders, traditional owners and African Australians, detailed police brutality against members of their own families and racism they had experienced.
Demonstrators were told to use hand sanitizer and wear masks, with organizers distributing masks among crowds.