1. To prepare sauce, heat oil in a large nonstick skillet over medium-high heat. Add onion to pan; sauté 3 minutes. Add garlic; sauté 1 minute. Add 1/2 cup water and next 5 ingredients (through tomato sauce). Cover and simmer 20 minutes. Uncover and simmer 5 minutes.
2. Preheat oven to 400°.
3. Heat a grill pan over medium-high heat. Coat pan with cooking spray. Add jalapeños to pan; cook 9 minutes or until tender and blackened, turning occasionally. Cut a lengthwise slit in each jalapeño; discard stems, seeds, and membranes.
4. Combine cream cheese and next 3 ingredients (through 1 garlic clove). Fill each jalapeño with about 1 tablespoon cheese mixture. Place jalapeños on a baking sheet coated with cooking spray. Bake at 400° for 7 minutes or until warm. Serve with tortillas and sauce.