Heat oil in large skillet over medium-high heat until shimmering. Cook onions, brown sugar and 1/4 teaspoon salt until onions are golden, 10-12 minutes. Stir in tomato paste and flour and cook until darkened, about 2 minutes. Add garlic and cook until fragrant, about 30 seconds. Stir in broth and cook until sauce thickens, about 4 minutes. Off heat, stir in 2 tablespoons vinegar and transfer mixture to bowl.
Combine 1 teaspoon salt, paprika, onion powder, garlic powder and cayenne in bowl. Using fork, prick brisket all over. Rub spice mixture over brisket and wrap tightly in plastic. Cover bowl with onion mixture with plastic wrap. Refrigerate brisket and bowl with onion mixture overnight.
The next morning, add half of onion mixture to slow-cooker insert. Add thyme and bay leaves and place brisket, fat side up, on top. Spread remaining onion mixture over brisket. Set slow cooker to low, cover, and cook until brisket is fork-tender, 9 to 10 hours (or cook on high for 5 to 6 hours). Turn cooker off and allow brisket to rest for 30 minutes.
Transfer brisket to cutting board, cut across grain into 1/2-inch slices, and transfer to serving platter. Tent with foil. Pour sauce into large skillet, discard herbs, and simmer over high heat until slightly thickened, 8 to 10 minutes. Skim fat, add remaining vinegar, then pour half of sauce over brisket. Serve with remaining sauce on side.