Survivors stood alongside friends and relatives of the 28 British victims as well as representatives from the 21 other nations which lost citizens including Australia, Indonesia, Germany, Switzerland, Portugal, Italy, Poland and Greece.
Names of all the dead were read during the hour-long ceremony at St James's Park.
The Prince was accompanied by the Duchess of Cornwall as he unveiled the memorial which comprises a marble globe with a carved dove to represent each of the victims. A minute's silence was held as part of the ceremony and afterwards the Prince laid a wreath made of poppies and his white fleur de lys. His tribute read: "With our heartfelt thoughts and prayers."
Two of the doves on the memorial represent Sheffield cousins Laura France, 18, and Natalie Perkins, 20, the youngest victims of the attack who were just a month into a round-the-world trip.
Natalie's father Tony Perkins travelled to the ceremony in London with his brother Jonathan. He said: "I think about Natalie every single day and I miss her terribly. My grief today is no different to how it was four years ago ... I have just learned to cope with it better.
"Your children should never die before you. It's the worst feeling in the world."
The British memorial has been jointly funded by the Government and the UK Bali Bombing Victims' Group. A spokeswoman for the group said: "This is a significant moment for all those affected by the bombings and in particular those who lost loved ones.
"Our aim in marking this dreadful tragedy is to provide a beautiful and fitting public and permanent memorial to the loss of so many innocent people."
Other ceremonies were held in Indonesia and Australia in memory of those who died in the attacks, carried out by militant group Jemaah Islamiyah, linked to al- Qaida.