Bring a large pot of salted water to a boil. Add the whole wheat penne pasta and cook according to package instructions until al dente, about 9-11 minutes. Drain and set aside.
While the pasta cooks, heat olive oil in a large skillet over medium heat.
Add the finely chopped onion to the skillet and sauté for 3-4 minutes until softened.
Add the minced garlic and cook for an additional 1 minute until fragrant.
Add the lean ground beef to the skillet. Cook, breaking it up with a spoon, until browned and cooked through, about 6-8 minutes. Drain excess fat if necessary.
Stir in the diced tomatoes with their juice, tomato sauce, dried oregano, dried basil, crushed red pepper flakes, salt, and black pepper.
Bring the sauce to a simmer, reduce heat to low, and cook for 10 minutes, stirring occasionally to blend flavors.
Add the cooked pasta to the skillet with the beef sauce. Toss gently to combine and heat through for 2 minutes.
Remove from heat and sprinkle grated Parmesan cheese and chopped fresh parsley over the pasta. Toss lightly to distribute.
Serve immediately while hot.