Preheat an oven to 350 degrees F (175 degrees C). Grease a 9×13 inch baking dish.
Bring a large pot of salted water to a boil. Add the pasta and cook to al dente according to package directions.
While the pasta is cooking, heat the oil in a large skillet over medium heat, and add the zucchini, squash, onion, red and green peppers, and garlic. Cook stirring occasionally until the vegetables are tender, for about 10 minutes.
Pour in the tomatoes, pasta sauce and stir to mix. Add red and black pepper to taste, and bring the mixture back to a boil. Simmer for 20 minutes.
Pour the vegetable mixture into the bowl with the cooked penne pasta, stir to mix well, and spoon into the prepared baking dish.
Sprinkle the mozzarella cheese over the top, and bake in the preheated oven until the cheese is melted and the casserole is bubbling, 20 to 30 minutes.