It'll be fine. Just put it in the refrigerator after the initial rise. That will slow the yeast considerably. (If you let it sit on the counter for three hours, yeah, it risks over-rising and becoming a mess on your counter.)
I usually make yeasted waffle dough the night before. That way, all I have to do in the morning is heat up the waffle iron and get cooking. You don't even need to bring it to room temperature before cooking. (I also leave yeasted bread dough in the fridge, for as long as a week, but they need to be brought to room temperature before baking.)
You might even prefer it that way. The yeast will continue to work, slowly, producing more yeasty flavors. That's a key component to the flavor of good sourdough.