"The 12 October 2002 tragedy shocked Australia. For those who lost loved ones, life will never be the same," Rudd said in the statement.
"We think of the families and friends of the victims. Our thoughts and sympathies will always be with them."
Rudd praised Indonesia for the crackdown it carried out in the wake of the worst attack in the region.
"We can be proud that the partnership between Indonesia and Australia is the strongest it has ever been," he said.
Sidney Jones of the International Crisis Group, told Al Jazeera that the crackdown on Jemaah Islamiyah has created more awareness about the group's activities.
"The best thing the government did was to bring those responsible for the attacks to full public trials and then the Indonesian public clearly saw this was a home grown Jihadist group," she said.
"It [Jemaah Islamiyah] is much weaker in term of political organisation, but it also needs to be seen as a social network, and it can't easily be broken up."
The anniversary was held amid a promise from the Indonesian government that Amrozi, Imam Samudra and Ali Ghufron - the three men convicted of carrying out the attacks - would be executed by the end of the year.
The three men, who have shown no regret for the attacks, promised "retribution" if they were executed.