No one on board the flight survived, but no one on the ground was harmed.
Heubner told the congregation of several hundred that September 11, 2001, was a rare day "that galvanised the collective hearts and minds of humanity".
The world watched on television "the brutal murders of 3000 humans from 90 different nations, people of all religious beliefs, all political viewpoints, young and old, men and women, gay and straight," he said. "Murdered by those preaching hatred simply to instil a fear and we reacted with near unanimous horror and sorrow."
Prime Minister John Key, who was not at the service, said in a message that September 11 "strengthened international resolve to fight terrorism".
He said the anniversary was particularly poignant in New Zealand because the United States team would be playing Ireland in the Rugby World Cup on the same day.
Eagles scrum-half Mike Petri was at school in Manhattan when hijacked aircraft ploughed into the World Trade Centre and recalled seeing the smoking rubble when he went home.
He said the emotion going into the Ireland match was "going to be intense".
"Watching the heroes running towards the tower to help as people ran away from them is an image that is with you forever.
"I was just lucky when I went home my family were still there. A lot of people I grew up with were not so lucky."
There was a minute's silence before the match on Sunday and both sides wore black armbands.
- AAP