Andrew Chan, 31, an Australian, became a Christian whilst serving ten years behind bars for drug smuggling.
Earlier this year he was ordained a pastor and last week he married an Indonesian pastor.
Last night he was killed by a 13-member firing squad along with eight other people.
A ninth person, a woman from the Philippines, was granted a stay of execution.
Revd Chan's brother, Michael Chan, said: "I have just lost a courageous brother to a flawed Indonesian legal system. I miss you already. RIP my Little Brother."
Mr Chan had previously said his brother was "dignified" in his final hours of life.
Australian prime minister Tony Abbott condemned the killings and announced that Australia is to withdraw its ambassador from Jakarta.
He said it was clear Revd Chan and the other Australian, Myuran Sukumaran, 33, had been "fully rehabilitated while in prison".
"These executions are both cruel and unnecessary," he added.
Revd Chan's mother Helen after visiting her son for the last time.
In a statement the families of the two Australians said: "In the ten years since they were arrested, they did all they could to make amends, helping many others. They asked for mercy, but there was none."
The rest of the people killed included four Nigerians, a Brazilian and an Indonesian man.
Brazil's president Dilma Rousseff said the execution "marks a serious event in the relations between the two countries".
Indonesian Attorney General Muhammad Prasetyo said: "What we're doing is carrying out court decisions."
He added the message of the killings was "do not try to smuggle drugs in Indonesia, because we will be harsh and firm against drug-related crimes".