Preheat the oven to 325°F (163°C).
Pat the beef chuck roast dry with paper towels. Season all sides evenly with kosher salt and freshly ground black pepper.
Heat vegetable oil in a large Dutch oven or oven-safe heavy pot over medium-high heat until shimmering.
Add the beef roast to the pot and sear it on all sides until deeply browned, about 4 minutes per side. Remove the roast and set aside.
Add the quartered onion, smashed garlic cloves, carrots, and celery to the pot. Cook, stirring occasionally, until the vegetables begin to brown, about 5 minutes.
Stir in the tomato paste and cook for 1 minute to deepen the flavor.
Pour in the beef broth and dry red wine, scraping the bottom of the pot with a wooden spoon to loosen any browned bits.
Return the seared beef roast to the pot. Add the rosemary, thyme, and bay leaves.
Cover the pot with a lid and transfer it to the preheated oven. Cook for 3 to 3 1/2 hours, or until the beef is fork-tender.
Remove the pot from the oven. Transfer the roast to a cutting board and tent with foil to keep warm.
Strain the cooking liquid into a saucepan, discarding the solids. Skim off any excess fat from the surface.
Place the saucepan over medium heat. In a small bowl, mix the all-purpose flour with 2 tablespoons of cold water to create a slurry.
Whisk the flour slurry into the cooking liquid and simmer until the sauce thickens, about 3 to 5 minutes.
Slice the beef roast against the grain and serve with the thickened sauce and cooked vegetables.