Heat oil in a large saute pan over medium-high heat. Add onions and saute for 5 minutes, stirring occasionally, until the onions are soft and translucent. Add garlic and saute for 1 minute, stirring frequently, until fragrant. Add in the tomatoes, tomato paste, basil, salt, pepper, and crushed red pepper flakes, then stir to combine. Continue cooking until the sauce reaches a simmer. Then reduce heat to medium-low and continue to let the sauce simmer for about 15 minutes, or until the oil on the surface is a deep orange and the sauce is reduced and thickened. Taste, and season the sauce with additional salt and pepper if needed.
Add in the spiralized zucchini and toss until it is evenly coated with sauce. Continue to cook for 2-3 minutes until the noodles are slightly softened. Remove from the heat and serve immediately, garnished with Parmesan cheese.