Combine first 5 ingredients in a small bowl; stir in 1/8 teaspoons salt. Scrap mixture into a zip-top plastic bag. Add chicken; seal. Marinate in refrigerator for 2 hours; turning after 1 hour.
Immerse 12 (8-inch) wooden skewers in water; soak for 30 minutes. Drain and pat dry,.
Preheat grill to medium-high heat. Remove chicken from marinade; discard marinade. Thread 3 chicken pieces, 1 pepper slice, and 1 tomato alternately onto each skewer, beginning and ending with chicken; sprinkle evenly with remaining 1/2 teaspoons salt. Arrange skewers on grill rack, coated with cooking spray, grill 4 minutes on each side or until done. Serve with yogurt.