The acidic ingredients and cooking time tenderize this tough cut of beef.
Heat oven to 350 F.
In a large Dutch oven or heavy pot, heat 1 tablespoon oil over medium-high heat. Season brisket with pepper. In batches, cook meat, turning occasionally, until dark brown on all sides. Transfer brisket to a plate.
Add onions to pot. Cook and stir until browned. Add garlic and thyme and cook and stir until fragrant, about 1 minute.
Add tomatoes (undrained), vinegar, and stock or wine. Bring to a boil. Return beef to pot, cover, then place pot in oven. Cook until beef is tender, 3 to 3 1/2 hours.
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