Trim excess fat from brisket. Rub brisket with 1/2 teaspoon salt and 1/2 teaspoon pepper. Brown brisket on both sides in hot oil in a large skillet over medium-high heat.
Place half of onion slices in bottom of a 6-quart electric slow cooker. Top with mushrooms. Combine red wine and next 4 ingredients; stir well. Drizzle half of red wine mixture over mushrooms; top with brisket. Place remaining half of onion slices on top of brisket. Drizzle with remaining red wine mixture. Cover and cook on HIGH 1 hour. Reduce to LOW, and cook 9 hours.
Remove meat to a serving platter; keep warm. Remove vegetables with a slotted spoon; set aside. Reserve 2 cups liquid in slow cooker.
Stir together flour and water until smooth; stir into reserved liquid. Cover and cook on HIGH 15 to 20 minutes. Add vegetables, remaining 1/4 teaspoon salt, and remaining 1/4 teaspoon pepper; stir well. Serve wine sauce over brisket.