Preheat the oven to 375°F (190°C).
Bring a large pot of salted water to a boil. Add the penne pasta and cook according to package instructions until al dente. Drain and set aside.
While the pasta cooks, heat olive oil in a large skillet over medium heat.
Add the diced onion and sauté for 3-4 minutes until translucent.
Add the Italian turkey sausage to the skillet, breaking it up with a spoon. Cook until browned and cooked through, about 6-8 minutes.
Add the minced garlic and cook for 1 minute until fragrant.
Stir in the marinara sauce, diced tomatoes, dried oregano, dried basil, crushed red pepper flakes, salt, and black pepper. Simmer for 5 minutes to combine flavors.
In a large mixing bowl, combine the cooked pasta and sausage tomato sauce mixture. Stir to combine evenly.
Lightly grease a 9×13-inch baking dish. Transfer the pasta mixture into the dish and spread evenly.
Sprinkle the shredded mozzarella cheese and grated Parmesan cheese evenly over the top.
Cover the baking dish tightly with aluminum foil if preparing ahead, or leave uncovered if baking immediately.
To make ahead: Refrigerate the covered pasta bake for up to 24 hours. When ready to bake, preheat the oven to 375°F (190°C) and bake covered for 25 minutes, then uncover and bake an additional 10-15 minutes until cheese is melted and bubbly.
If baking immediately: Place the uncovered pasta bake in the preheated oven and bake for 25-30 minutes until cheese is melted and bubbly.
Remove from the oven and let cool for 5 minutes before serving.
Garnish with fresh basil leaves if desired.