It isn't about the size of their ad, it's about what your photo is worth.
Are you an industry professional who gets paid to take photographs? Do you have a high level of skill? Did you plan to use the photo to sell to other publications for income?
How did they get their hands on the image? Did you post it on an image share site, like Facebook or Flickr for the world to see? If you were planning to use the image to market to make money, you would not have uploaded a high-res image without a watermark to a place where anybody can save it and use it.
Is it a large company or a small company? Have they done this before? Do you have sufficient time and money to pursue a (potetially) legal fight to claim money from them? Is the photo particularly exceptional? Does the image contain people who have not signed an advertising release form?
All of these things need to be taken into account before you issue an invoice for unauthorised use of your photograph. You will need to provide them with evidence that the original image was yours and that their advertising agency used it without permission. You will need to draw up a clear contract to attach to the invoice to clarify whether :
>> you are charging them for the one-time use of the image retroactively,
>> whether you are claiming damages from them (their use of the image has negated the income you would have received from selling the image to someone else) and
>> whether by them paying you you are authorising them to continue using your image in future advertising campaigns.
You are probably not going to get more than a few hundred rand out of the image, maybe R1000 at most (if I had to take a guess from your question about the pricing to begin with). The first step in any of this is to contact the company and inform them that they used your image without authorisation. It's very likely that the lazy designer who created the ad just grabbed your pic and used it without the company even being aware that it was unauthorised. Your fight is probably going to be with the ad agency, not the company themselves. You need to first understand exactly who you're trying to claim from.
Good luck. Best you'll probably get is an apology.
Edit: I've checked out your gallery and I see you've got some really great photos in there. You obviously do do this either professionally or as a serious amateur with skills. Some extra questions this raises are:
>> Was the image used one you were contracted to take? Or did you just snap it on your own?
>> Are the people who used the image in an ad the owners of the object in the picture? (eg I see you have a lot of pics of racing cars - the owners of the racing car might have more right to make use of a pic you took of their car than a nature mag making use of the pic you took of a bird).
>> You mark most of your images - did the person who took and used the ad purposely crop your signature or watermark out of the image?
I still believe it comes down to you working out how much the image is worth to you - to sign away your future sales rights on that image used. As a pro you know what you charge for images, so work out a rate that seems reasonable to you and submit an invoice to them.
If they do pay you, remember to declare it in your tax 
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