Adjust rack to lower-middle position and heat oven to 450 degrees. Toss short ribs evenly with oil and a light sprinkling of salt and pepper.
Meanwhile heat a heavy-bottomed Dutch oven or soup kettle over medium-high heat. Working in two batches to avoid overcrowding, add short ribs to hot pan. Cook each batch, turning only once, until well-browned on each side, 5 to 6 minutes.
Drain all but 1 tablespoon of the fat from the pan. Add onion; sauté until lightly brown and translucent, about 5 minutes. Add garlic and thyme, sauté until fragrant, about a minute. Stir in flour, then wine, followed by chicken broth and tomatoes. Return short ribs to the pot and bring to a simmer.
Place a sheet of heavy-duty foil over pot. Use a potholder to press down foil so that it touches stew. Seal foil completely around edges. Place lid snugly on pot. Place pot in oven and cook until ribs are fall-off-the- bone tender, about 1½ hours.