Preheat the oven to 375°F (190°C).
Bring a large pot of salted water to a boil. Cook the penne pasta according to package instructions until al dente. Drain and set aside.
In a large skillet, heat the olive oil over medium heat. Add the Italian turkey sausage, breaking it up with a spoon, and cook until browned and cooked through, about 6-8 minutes.
Add the chopped onion to the skillet and cook until softened, about 4 minutes.
Stir in the minced garlic and cook for 1 minute until fragrant.
Add the crushed tomatoes, tomato paste, dried oregano, dried basil, crushed red pepper flakes, salt, and black pepper. Stir to combine and simmer the sauce for 10 minutes, stirring occasionally.
In a large mixing bowl, combine the cooked pasta and the sausage tomato sauce. Mix well to evenly coat the pasta.
Lightly grease a 9×13-inch baking dish. Spread half of the pasta mixture evenly in the dish.
Sprinkle half of the shredded mozzarella and half of the grated Parmesan cheese over the pasta layer.
Add the remaining pasta mixture on top, then sprinkle the remaining mozzarella and Parmesan cheeses evenly over the top.
Cover the baking dish tightly with aluminum foil and refrigerate if making ahead. When ready to bake, preheat the oven to 375°F (190°C).
Bake the pasta bake covered for 25 minutes. Remove the foil and bake for an additional 10-15 minutes, or until the cheese is melted and bubbly.
Remove from the oven and let stand for 5 minutes before serving.
Garnish with chopped fresh parsley and serve warm.