Preheat the oven to 325°F.

Season the short ribs generously with salt and pepper. In a large Dutch oven or oven-safe pot, heat olive oil over medium-high heat. Brown the short ribs on all sides, about 3-4 minutes per side. Transfer to a plate and set aside.

In the same pot, add onion, carrots, and celery. Sauté until vegetables are softened, about 5 minutes. Add garlic and cook for another minute.

Pour in red wine to deglaze the pot, scraping up any browned bits from the bottom. Allow wine to simmer for 5 minutes. Stir in the canned tomatoes, beef broth, bay leaves, and thyme.

Return the short ribs to the pot, ensuring they are submerged in the liquid. Bring to a simmer, then cover and transfer the pot to the preheated oven.

Braise in the oven for about 2.5 to 3 hours or until the short ribs are tender and falling off the bone.

Remove the short ribs from the pot. If desired, strain the cooking liquid and vegetables through a fine-mesh sieve for a smoother sauce, then reduce the sauce further on the stove if a thicker consistency is desired. Season sauce with salt and pepper to taste.