In bowl of blender, add 1 can black beans, chipotle chile and sauce and 2 cups water. Puree until smooth, about 30 seconds; set aside.
Heat oil in large pot over medium-high heat. Add onions and peppers; cook until soft, about 10 minutes. Add garlic and cumin; cook until fragrant, about 30 seconds more. Add chicken bouillon mixture, reserved black bean puree and remaining black beans; bring mixture to a boil; reduce heat to medium low and cook, stirring occasionally, until soup thickens and flavors come together, about 10 minutes.
Divide soup evenly among serving bowls. Top with a dollop of sour cream. Sprinkle with tomatoes and cilantro.