Foreign royals, including the Crown Prince of Japan, attended the coronation ceremony in the capital, Nuku’alofa.
A retired Australian minister performed the crowning as it is taboo for Tongans to touch their king’s head.
Former King George Tupou V died in March 2012.
The coronation was the culmination of a week of festivities that included a traditional drinking rite, street parties and feasts.
The ceremony, performed by 78-year-old retired Methodist minister D’Arcy Wood, drew thousands of Tongans and tourists.
As well as Crown Prince Naruhito, the European royals Prince Georg von Habsburg of Hungary and Princess Marie-Therese von Hohenberg of Austria attended.
Tupou VI, 55, ascended to the throne after his bachelor brother died.
Tonga gained its independence from Britain in 1970 but the monarchy stretches back 1,000 years.