The shoes underwent a preservation process that took over a year of work at the Auschwitz Museum Conservation Laboratories.
Biden will report on the results of his strategy to combat antisemitism, rolled out a year ago.
In the hope of preventing disturbances on Saturday, total capacity at the central Dam square will be limited to 10,000 - roughly half the normal attendance at the ceremony, the city said.
"We will do everything possible to ensure that the facts are investigated and the perpetrators are punished," the community said in a statement.
"The protestors showed their true colors. This is antisemitism, plain and simple," Combat Antisemitism Movement CEO Sacha Roytman stated.
Among the exhibits at the site are a reproduction of sleeping cells from the Auschwitz death camp, artifacts and documents that belonged to survivors who fled the Nazis to Porto.
The event was subsequently canceled, per an announcement on social media platform X
The ceremony featured the lighting of a memorial flame in front of 500 students from schools across Portugal who took part in the event.
A report by a leading medical journey says that all health professionals must study the history of the central role taken by doctors in antisemitic, racist and barbarous crimes.