Yes. A return envelope marked "confidential" is included with the form for you or your doctor to use to return your medical certification to OHR. Medical certifications are kept in a separate, locked cabinet, apart from your personnel file.
Your supervisor does not receive a copy of the medical certificate. OHR shares only information that is consistent with business necessity (i.e., the date your leave begins, the date your leave ends, and whether you will be off intermittently or will work reduced hours) with your supervisor.