Here's my method with Photoshop. First off, forget using the burn tool, it will wash out the colors and definition of the nipples. Secondly, this method will get results more often (albeit, not all the time) even on thicker cloth like bikinis.
The biggest factors in getting results are:
You can now use this modified graphic on top of the original photo with different blending modes and other Photoshop magic to bring the color back.
One thing to look out for: depending on the folds, seams, and shadows of the clothes, it might come together in such a way that it makes something appear like a nipple when in actuality it is not; so double check. Use common sense to locate where a nipple should logically be located.