Will my overstay in South Africa be noticed?

From the South African high commission website:

Any foreigner who leaves the Republic after the expiry of his or her permit shall be liable to an administrative fine of a prescribed amount not exceeding R3000.00 which fine shall be imposed by the Department on detection of the overstay and exacted when such foreigner is admitted or makes an application with the Department.

Failure to pay the prescribed fine will mean that a foreigner will not be admitted to South Africa, or issued with a Visa or Permit or if already admitted, a permit shall not be issued or renewed nor a subsequent permit issued.

So yes, there's a penalty, but while frustrating it's not the end of the world. Certainly no jail time, by law. You definitely want to make sure they know about it and pay the fine, however, as if it's discovered AFTER you leave and you've not paid, you'll potentially be barred from ever reentering. And yes, you may not think you'll return to South Africa, but do you really want to rule that out of the rest of your life?

Whether or not they'll find it is probably subjective, but you can probably at least play the sympathy card with the passport being stolen and so on - give them the details, and if you get the right person they may even reduce the fine, or remove it.

But definitely, pay it, don't try to avoid it.

EDIT: Went hunting for more information.

From South Africa House in the UK (updated October 7, 2014):

A person who overstays after the expiry of his or her visa, as contemplated in section 30(1)(h) of the Act, may:

• In the case of a person who overstays for a period not exceeding 30 days, be declared undesirable for a period of 12 months;

• In the case of a person who overstays for the second time within a period of 24months, be declared undesirable for a period of two years; and

• In the case of a person who overstays for more than 30 days, be declared undesirable for a period of five years.

So from there, it seems it may depend on how long you overstayed, but again, no jail.

On the same page, an appeals process is provided, if you wish to make a case to return earlier.

Recently, Zimbabweans have been given a reprieve for overstaying.

The Department of Home Affairs lists a process for appeals for overstaying.

I overstayed by two hours (missed my flight connection in Joburg) and I'm banned for a period of 12 months. However, I did't get a fine. I would have absolutely loved to pay the fine, because now i'm not able to visit my fiancé in SA up until Januari 31 2016.

My advice: pay the fine, especially when you met someone there.

Since they changed the regulations in June 2014, they don't make you pay a fine anymore but you become an undesirable person for up to 5 years. Happened to me too, and I also have a fiancé there. I appealed 3 months ago and havn't heard back yet.