Use disease-free seed. There's no evidence that this fungus is carried by seeds, but err on the safe side and don't save seed from infected plants. Thoroughly processing the tomato seeds you are saving will also help rid the seeds of lingering diseases.
Start with a clean garden. Dispose of all affected plants. The fungus can over-winter on the debris of diseased plants. It's important to dispose of all the affected plants far away from the garden and the compost pile. Keep in mind that it may have spread to your potatoes and eggplants, too.
Avoid overhead watering. Water aids the spread of Septoria leaf spot. Keep it off the leaves as much as possible by watering at the base of the plant only. Of course, it's impossible to keep the rain off your plants, but every little bit helps.
Provide room for air circulation. Leave some space between your tomato plants so there is good airflow. Stake them so that they are not touching the ground and not all bunched together. Good air circulation is especially important during damp and rainy periods.
Mulch below the plants. A layer of mulch will help prevent spores on the ground from splashing up onto the lower leaves.
Plant next year's tomatoes in a different section of your garden. In small gardens, it's not always practical to rotate your crops, so good clean up and sanitation become even more important.