Put diced onion, garlic, and mushrooms in a large stock pot with a few tablespoons of water. Stir over high heat until onions are soft.
Add crushed tomatoes, water, beans, basil, oregano, pepper and rosemary to the onion mixture. Add penne or your choice of pasta, heat to boiling, then turn heat to medium-low. Stir frequently while pasta cooks, about 10 minutes, depending on the package directions.
While pasta cooks, blend milk, yeast, and reserved beans together until creamy.
When pasta is finished, remove from heat. Stir in spinach and yeast sauce. Serve hot.