Masses have been held in cities around the country to mark the execution.
In Melbourne, the bell tolled 25 times at St Ignatius Catholic Church in Richmond - once for each year of Nguyen's life.
Members of Victoria's Criminal Bar Association gathered outside the County Court in Melbourne to observe a minute's silence for Nguyen.
Stephen Shirrefs, the vice-chairman of the association, says they support the fight against the mandatory death penalty.
'We are here to demonstrate our opposition to capital punishment, as a mark of respect to the family of Van Nguyen and as a mark of solidarity for two of our members who in the fine tradition of the Victorian Bar have acted pro bono and for the last three years fought to save the life of Van Nguyen,' he said.
At Martin Place in Sydney, a Vietnamese gong also sounded 25 times.
A crowd gathered and maintained a silent vigil.
Churchgoers in Brisbane have also prayed for Nguyen and expressed hopes the events of today are not taken for granted.
Fr Peter Dillon led the congregation at St Stephen's Cathedral in a prayer calling for an end to executions.
Fr Dillon says he fears today's execution will have little impact on the drug trade.
'I sadly think, unfortunately, and this is the insidiousness of the drug culture, I think it's just another dead body for the drug world. And there's thousands of them everyday, so I don't think they're going to be moved by all this,' he said.
This is desperately sad for the country as well as Van Nguyen's immediate family. That the most Singapore can bring itself to allow is for Nguyen's mother to touch him through a wire grill speaks volumes about the degree of compassion they have exhibited.
Singapore is entitled to its own laws. So is Australia. In future dealing with them, especially on criminal matters, the Australian government should remember that Singapore maintains this repugnant law. Capital punishment is wrong in itself. Capital punishment as a mandatory sentence should shock the conscience of everyone. Singapore has not ratified the International Covenant of Civil and Political Rights.
ICCPR Article 6
1. Every human being has the inherent right to life. This right shall be protected by law. No one shall be arbitrarily deprived of his life.
2. In countries which have not abolished the death penalty, sentence of death may be imposed only for the most serious crimes in accordance with the law in force at the time of the commission of the crime and not contrary to the provisions of the present Covenant and to the Convention on the Prevention and Punishment of the Crime of Genocide. This penalty can only be carried out pursuant to a final judgement rendered by a competent court.
3. When deprivation of life constitutes the crime of genocide, it is understood that nothing in this article shall authorize any State Party to the present Covenant to derogate in any way from any obligation assumed under the provisions of the Convention on the Prevention and Punishment of the Crime of Genocide.
4. Anyone sentenced to death shall have the right to seek pardon or commutation of the sentence. Amnesty, pardon or commutation of the sentence of death may be granted in all cases.
5. Sentence of death shall not be imposed for crimes committed by persons below eighteen years of age and shall not be carried out on pregnant women.
6. Nothing in this article shall be invoked to delay or to prevent the abolition of capital punishment by any State Party to the present Covenant.
The federal parliament should make laws to prohibit police assistance where capital punishment is a possibility or where the other country has not signed and ratified the ICCPR. Article 6 is now the minimum standard in any decent nation. Article 6 should be the only standard on which we will extend criminal assistance to other nations and Section 8 of the Mutual Assistance In Criminal Matters Act 1987 should be amended accordingly. Anyone using Optus or Singapore Airlines should find another company that is not owned by executioners.
12 other Australians face the possibility of execution in Bali, Vietnam and Kuwait.