Thanks for the query.
From the internet I come to know that the highest capital city is La Paz (and Sucre), the capital cities (La Paz - the seat of the country's government. Sucre - the constitutional capital) of Bolivia. The altitudes of the cities are - 3640 m (11,942 ft) and 2750 m (9,022 ft).
Source - https://en.wikipedia.org/wiki/List_of_capital_cities_by_altitude
Where is the World Heritage city, once a capital in Nabataea and now a major archaeological site for Roman, Byzantine and Muslim ruins with further ancient Nabataean and Roman monuments, Christian churches, mosques and Madrasas?