Understanding the role of defects in the magnetic properties of the graphene buffer layer (BL) grown on substrates should be important to provide hints for manufacturing future graphene-based spintronic devices in a controlled fashion. Herein, density functional theory was applied to assess the structure and magnetic properties of defective BL on 6H-SiC(0001). Particularly, we conducted a thorough study of one and two vacancies and Stone-Wales defects in the BL. Our results reveal that the removal of a carbon atom in the BL framework that was originally bonded to a Si atom in the substrate is preferred over that of a sp2-bonded atom. As a result, a hexacoordinated silicon atom is formed with a slightly deviated octahedral geometry. A stable antiferromagnetic (AF) state was verified for the single vacancy system, with a quite different spin-density distribution to the one obtained for the perfect BL. Also, this AF state is nearly degenerate with the non-magnetic and low magnetic states. As for the Stone-Wales defect, the AF sate is almost degenerate with the most stable M = 2 μB magnetic configuration. However, the introduction of two vacancies in the carbon network of BL causes the loss of magnetism of the BL-SiC system. Our theoretical calculations support experimental predictions favoring the BL as the site for single vacancy formation rather than the epitaxial monolayer graphene, by 4.3 eV.