Victoria Police arrested 62 protesters, some for assaulting police, but most for breaching public health orders.
“I implore you to stay home,” Victoria Police Chief Commissioner Shane Patton said on Tuesday night.
“Our tactics tomorrow will be different.”
It is not clear if demonstrators are all union members, with CFMEU Victorian construction secretary John Setka blaming “neo-Nazis and right-wing extremists” for hijacking the event.
Premier Daniel Andrews and other unions have labelled the protest as selfish.
“There is no excuse for the terrible behaviour we have seen in our city over the last two days,” Mr Andrews said.
“Acts of violence and disruption won’t result in one less case of Covid – in fact, it only helps the virus to spread.”
The ambulance union pleaded with protesters to think of others.
“The fight against COVID-19 is not in the street. For our health workers the fight is very real, very exhausting, very painful and very dangerous,” the union said in a statement on Tuesday night.
“You are thinking of yourself only. There has never been a more important time to match the selflessness of health workers, with your own.”
The state government has shut down the construction industry for two weeks in metropolitan Melbourne, City of Ballarat, City of Greater Geelong, Surf Coast Shire and Mitchell Shire.
Victoria on Tuesday reported 603 new COVID-19 cases – its highest daily tally in the current outbreak and since August 2020 – and one death.