Does the non-resident speculation tax still apply if a work permit holder buys jointly with a Canadian spouse?

Generally, no - Ontario's Non-Resident Speculation Tax includes a specific exemption for purchases made jointly with a spouse who is a Canadian citizen or permanent resident, and this can apply even where the other spouse is a foreign national on a work permit who would otherwise be subject to the tax buying on their own. The reasoning behind this exemption is that a couple settling together, where one spouse already has Canadian status, is treated differently than a purely foreign, non-resident purchase.

This exemption is specifically about the marital or equivalent relationship and joint purchase structure, not about the work permit holder's employment status itself, which is a distinct and, on its own, insufficient basis for exemption, addressed in a related question. Getting the purchase structured correctly, and properly documenting the spousal relationship and citizenship or permanent residency status, matters for actually securing this exemption at registration.

Confirm with your lawyer that the purchase is structured to properly reflect the spousal relationship and Canadian status, so the exemption is correctly applied when the transfer is registered.