So, your tomato is ripe and ready to eat. Then why are the seeds germinating? There are several reasons this can happen, but most importantly the tomato with germinated seeds can be eaten safely.
Seeds germinating inside a tomato is called vivipary. It occurs in overripe fruit when seeds have reached maturity and the natural hormone, abscisic acid (ABA), is reduced. Then, seed dormancy is lost gradually. The tomato fruit allows vivipary since the seeds do not desiccate (dry out) in the moist environment inside the fruit.
Some causes of seeds sprouting in tomatoes are long storage in cool temperatures (below 55 degrees), being overripe, potassium deficiency, over fertilization with nitrogen and again, being overripe, the predominant causes of vivipary.