Trim fat from brisket; place in a 13 x 9-inch baking dish. Sprinkle top of brisket with 1/2 teaspoon pepper; arrange onions over brisket.
Combine chili sauce, brown suagr, garlic, and beer, and pour over brisket. Cover, and bake at 350 for 3 hours. Uncover, and bake an additional 20 minutes or until brisket is tender. Place brisket on serving platter, reserving cooking liquid. Set brisket aside, and keep warm.
Pour 1 1/2 cups cooking liquid into a small saucepan. Place flour and salt in a bowl. Gradually add water, blending with a whisk; add to saucepan. Bring to a boil, and cook 2 minutes or until gravy is thickened, stirring constantly.
Serve gravy with brisket. Sprinkle with pepper, if desired.