The Supreme Court of Canada's decision to overturn the Alberta Court's acquittal had nothing to do with the notwithstanding clause. The notwithstanding clause, Section 33 of the Charter, is a clause used by legislative bodies to opt out of certain sections in the event a bill requires the denial of certain rights.

The Keegstra decision was based on Section 1 of the Charter, which states that the rights set out in the Charter, including freedom of expression, are subject to reasonable limits. The court decided that it was a justified denial of freedom of expression because of the harm that hate crime caused in society. Section 319(2) of the Criminal Code was thus "saved" by the Charter and reasonable limits and Keegstra charged under it.