Preheat your oven to 350°F (175°C) so it is hot and ready when the beans are assembled.
In a large bowl, combine the tomato sauce, ketchup, packed light brown sugar, molasses, yellow mustard, apple cider vinegar, Worcestershire sauce, smoked paprika, chili powder, garlic powder, onion powder, salt, black pepper, and water.
Whisk the mixture until the brown sugar and molasses are fully dissolved and the sauce looks smooth and evenly blended.
Add the cooked pinto beans to the bowl and gently stir until all of the beans are evenly coated in the smoky sauce.
Fold in the chopped cooked smoked brisket, distributing it evenly so every scoop of beans will have tender pieces of brisket.
Transfer the brisket bean mixture to a lightly greased 9x13 inch baking dish or similar oven-safe casserole, spreading it into an even layer.
Place the baking dish on the center rack of the preheated oven and bake uncovered for 60 to 75 minutes, or until the sauce has thickened and is bubbling around the edges.
Carefully remove the baked beans from the oven and let the dish rest for about 10 minutes so the sauce can settle and the flavors can meld.
Stir the brisket baked beans gently before serving, then spoon into bowls or onto plates and enjoy while hot.