Place beans in a Dutch oven; add water 2 inches above beans. Bring to a boil. Boil 1 minute; cover, remove from heat, and let stand 1 hour. Drain.
Bring beans, 4 2/3 cups water, and next 4 ingredients to a boil in Dutch oven. Cover, reduce heat, and simmer, stirring occasionally, 1 hour and 30 minutes or until tender. Add tomato and jalapeno pepper, and simmer mixture for 30 more minutes.