Heat the olive oil in a large skillet, over medium heat. Add the zucchini and shallots and cook until softened, about 10 minutes. Add the garlic and cook for another minute, until fragrant.
Add the pasta to the boiling water and cook until just al dente.
Reserve 1/4 cup of the pasta water from the pasta then drain and rinse the noodles.
Stir ¼ cup of the reserved pasta water, cream cheese, nutritional yeast, basil leaves, salt, and pepper into the zucchini mixture. Bring to a simmer and cook, stirring until the sauce has thickened, about 10 minutes.
Transfer the sauce to a high speed blender and blend on high until smooth.
Pour the sauce back in the skillet and add the pasta. Cook on medium heat for 2-3 minutes and toss well.