Heat oil in large Dutch oven on medium. Add onion and cook, stirring occasionally, 5 minutes.
Add carrots, celery, fennel, ¾ teaspoon salt, and ½ teaspoon pepper and cook, covered, stirring occasionally, until vegetables are beginning to soften, 6 to 8 minutes more.
Stir in garlic and thyme and cook 2 minutes.
Add wine and simmer until nearly evaporated, 1 to 2 minutes.
Add tomatoes and their juices, crushing them into small pieces as you add them to the pot.
Add 5 cups water and chicken base (if using) and bring to a boil.
Add pasta and simmer, stirring often, until barely tender, 8 to 12 minutes depending on type of pasta.
Stir in beans and cook until heated through, about 2 minutes.
Remove thyme and serve sprinkled with parsley and Parmesan.