If you have received the nomination certificate and not just NOI then you are exempt from the tax.
"An exemption from the NRST may be available in the following situations:
- Nominee – A foreign national who is nominated under the Ontario Immigrant Nominee Program (nominee) at the time of the purchase or acquisition, and the foreign national has applied or certifies that they will apply to become a permanent resident of Canada"
Doesn't say you must have used the certificate, just that you have one and have applied for PR.