Superior Court Judge Constance Sweeney's ruling allows the lawsuits accusing the archdiocese of ignored allegations of clergy abuse to go forward.
Attorneys from both sides have said they continue to hope the lawsuits can be settled out of court.
Church officials argued in court last month that the separation of church and state bars civil courts from getting involved in how church officials supervise priests.
The archdiocese has said the legal challenge on First Amendment grounds was required to satisfy its insurance carriers that it had done everything possible to defend itself against the lawsuits. Church officials hope that at least a portion of any settlement costs, estimated at millions of dollars, will be covered by insurance.
Lawyers for alleged victims said church officials were trying to avoid being held responsible and argued that the separation of church and state does not protect the conduct of church supervisors or priests.
"This recognizes that the church — merely by its status as a religious institution — is not above and beyond the law," said attorney Roderick MacLeish Jr., whose firm represents 270 alleged victims.
The archdiocese did not immediately return a call seeking comment.
The scandal has rocked the nation's fourth-largest diocese for the past year and led to questioning of church practices across the country. Boston's longtime archbishop, Cardinal Bernard Law, stepped down in December after calls for his resignation over his handling of abuse allegations.