City legislators and members of the Green Party and the AIDS activist group Act-Up were among the protesters sitting and lying down on the pavement as Paris Mayor Bertrand Delanoe led a ceremony formally renaming the square.
"Delanoe is honoring an assassin," some chanted, saying John Paul's opposition to condoms, along with other forms of contraception, was responsible for hundreds, even thousands of deaths to AIDS and other diseases.
Delanoe, joined by Paris Archbishop Andre XXIII, honored the late pope as a "messenger of peace."
"Was there another pope before him who had as much courage to talk about the Church's mistakes about the Holocaust, about the treatment of blacks, about the Crusades, about the wars of religion?" Delanoe asked.