Place the pumpkin, sweet potatoes, onion, ginger and garlic in a large pot. Pour in enough water to cover the vegetables. Bring to simmer over medium heat and cook until vegetables are tender and can be easily pierced with a fork, 30 to 45 minutes.
Remove pot from heat. Place soup in batches into a blender or the bowl of a food process. Pulse until smooth. Return soup to pot, and whisk in yoghurt. Season with salt and pepper to taste. If necessary, reheat soup over low heat, but do not allow to boil.