Spray a saucepan with cooking spray. Add garlic and cook over medium heat just until fragrant, about 1 minute. Add water, onion soup mix, and beef base; bring to a boil. Cover the pan and simmer until onions are tender, about 20 minutes.
Combine milk and flour in a jar with a lid; shake until combined and whisk into the saucepan. Bring gravy back to a boil and cook until thickened, about 10 minutes. Season with black pepper.