Heat a large skillet (preferably cast-iron) over medium heat. Cook the chilies, turning once, until they darken slightly and begin to puff, 1 to 2 minutes. Let cool slightly. Stem, seed, and tear into large pieces.
Combine the chilies, tomatoes, onion, garlic, vinegar, 1 cup water, and ½ teaspoon each salt and pepper in a large saucepan. Bring to a boil over medium-high heat. Reduce heat, cover, and simmer until the chilies are completely softened, 20 to 25 minutes. Uncover and cook until the liquid has thickened, 10 to 15 minutes.
Puree in a blender until smooth.