"Where football is involved I do not have the luxury of being a bystander," Khoza said in a statement.
"When approached to serve I am duty bound to give the matter serious consideration. I did indicate, when approached to stand, the limitations brought about by Article 37.9 of the Safa Constitution."
Khoza, who also serves as chairperson of the Premier Soccer League (PSL), referred to the clause which prevented anyone from holding the SAFA presidency while also holding an interest in a local club side.
The Zululand Region of SAFA raised the matter at a meeting held last Saturday and wanted clarity on the issue. They claimed it was common practice in football associations to have club owners serving on the committee and the matter was put up for discussion at a later date.
With the matter not yet resolved, Khoza could not be considered for the position.
"My standing at this stage will create a negativity that I can't afford to bring to football.
"I take this opportunity to thank those that approached me to stand. I derive continued strength in their confidence in me and the contribution they believe I make."
Incumbent president of SAFA, Kirsten Nematandani, is expected to face stiff competition for his position at the September 28 elective congress, after former SAFA chief executive Danny Jordaan was nominated earlier this week.
On Wednesday, Jordaan was nominated by 32 of the mother body’s 52 regions as their candidate to challenge Nematandani.