Collecting The Eggplant Seeds
Slice the overripe eggplant into cubes and separate the flesh from the seeds. A lot of the flesh will still be attached to the seeds, gently mashing up the pulpy seeds in a blender or even by hand will help separate more of the pulp. Pour this pulp and seed mix through a strainer with a fine enough mesh to catch the tiny eggplant seeds.
Agitate the pulp and seed mix to dislodge as many more seeds as possible, which will settle on the bottom. This process can be repeated multiple times as you will probably never get all the seeds, but as many as possible.
Storing the Seeds
Make certain the seeds are completely dry before storing them. Moisture easily leads to mildew which will destroy the seeds viability. Drying them off by placing them on absorbent paper towels or even coffee filters, followed by treatment with a hair dryer on a low setting works for me. Store them in a dry dark location for another 2 to 3 weeks before packaging them for winter storage.
Put the seeds in a airtight sealed jar [A zip lock plastic bag also works.] for winter storage. The reason for the jar is so you can monitor the humidity. If you notice any condensation on the inside of the jar - then there is unwanted moisture within the seeds. They could potentially grow mold or mildew.
Silica Gel works well for helping to keep stored seed dry. Silica gel is beads of amorphous silicon dioxide. Clear silica gel is packaged with many food and non food products and labeled 'do not eat.' Placing these in the jar with your seeds is advisable.
When properly stored eggplant seeds will be viable for up to 6 years.