Arrange half of cucumber in a 9-inch pie plate. Top with half of onion. Repeat procedure with remaining cucumber and onion.
Combine vinegar and next 5 ingredients (vinegar through chiles) in a small saucepan. Bring to a boil; cook 1 minute or until sugar dissolves, stirring occasionally. Pour hot vinegar mixture over cucumber mixture. Cover and marinate in refrigerator 1 to 4 days.
Arrange tomato slices on a platter; sprinkle evenly with 1/8 teaspoon salt and black pepper. Remove cucumber mixture from marinade with a slotted spoon; arrange over tomato slices.