Ambulances carrying coffins arrived at the prison island as relatives paid final visits to their condemned loved ones earlier today.
The nine inmates, all convicted on drug charges, were given 72-hour notices over the weekend that they would be executed by a firing squad, prompting a flurry of last-minute lobbying by foreign leaders.
The United Nations has argued that their crimes - ranging from possession of 72kg (11.3 stone) of marijuana to heroin trafficking - are not egregious enough to warrant the ultimate punishment.
Eight of the prisoners were executed at Besi prison on the island of Nusakambangan. A Filipino woman was spared at the 11th hour.
Among those executed were Australian nationals Andrew Chan and Myuran Sukumaran. Three Nigerians, one Brazilian, a Ghanaian and several Indonesian nationals were also among those believed to have been put to death.
The prisoners, all clad in white, were tied to poles in the jungle and shot dead by firing squad.
Earlier today, the condemned individuals were allowed time to see their loved ones before they were executed.
"I saw today something that no other family should ever have to go through,” Michael Chan of Australia, the brother of Andrew Chan, told journalists after saying farewell to his brother in prison.
"Nine families inside a prison saying goodbye to their loved ones. Kids, mothers, brothers, cousins, sisters, you name it, they were all there. To walk out of there and say goodbye for the last time, it's torture."
The execution of Filipino woman Mary Jane Fiesta Velos was stayed after the individual who allegedly recruited her as a mule came forward and confessed, reports suggest.
A dozen ambulances, nine carrying coffins, were driven onto the ferry to Nusakambangan. On the dashboard of one ambulance was a piece of paper bearing the name of Veloso.
Over the weekend, authorities asked the nine inmates - the two Australians and Veloso, as well as four Nigerian men and one man each from Brazil and Indonesia - for their last wishes and gave them a 72-hour notice of their executions.
Today, Australia's foreign minister defended Prime Minister Tony Abbott against online criticism that he had not done enough to save the lives of Sukumaran and Chan.
Australian actors including Geoffrey Rush, Guy Pearce, Joel Edgerton and Bryan Brown launched an online video calling for Indonesia to show mercy to the two men.
"Tony, if you have any courage and compassion, you'd get over to Indonesia and bring these two boys home," actor Brendan Cowell said to the prime minister.
But Australian foreign minister Julie Bishop said the Australian government was acting on advice from Australian diplomats in Jakarta who were part of a sustained campaign seeking a stay of execution.
"Clearly if travelling to Indonesia would make a difference, we would have gone there," Ms Bishop said.