I am associated with my spouse and my brother in a family SCI subject to IR. With my spouse, we occupy one of the properties of the SCI as our main residence. The SCI has decided to sell this property (...)

Will the 3 partners be exempt from real estate capital gains?

No. Capital gains realized on the sale of the main residence of the seller on the day of the sale are exempt (article 150 U, II-1° of the General Tax Code).
When the property is held through a company, it is first necessary to check what its tax status is.
Family SCIs are most of the time endowed with tax transparency, they are deemed for tax purposes not to have a separate personality from that of their partners (article 1655 ter of the CGI).The capital gain generated by the SCI during the sale of the property is therefore in principle taxed to each partner for the share which is due to him, in view of his participation in the share capital of the company.
If the property sold was your principal residence at the time of the sale, you, and your spouse benefit from the exemption. On the other hand, your brother will be taxed for the capital gain realized.