Heat oven to 325 degrees and adjust oven rack to lower-middle position.
Combine sugar, 1 tablespoons chipotle, cumin, and garlic powder in bowl. Rub mixture all over brisket and season with salt and pepper.
Combine onions, tomato paste, garlic, and oil in 12-inch skillet and cook over medium heat until onions are softened, about 5 minutes.
Add water, vinegar, and mustard and bring to simmer. Transfer brisket to carving board, tent loosely with foil, and let rest for 20 minutes.
Using large spoon, skim fat from surface of sauce. Whisk in remaining 1 tablespoon chipotle. Slice brisket across the grain into ½-inch-thick slices and serve, passing sauce separately.