The pair were in second spot throughout the 10-race 29er series but were pushed back to fourth when they lost a protest after the final race.
The third-placed Australian crew of Keiran Searle and Sam Phillips protested after the Dunedin boat touched the last mark in the last race.
The crew finished 16th in that race for their worst performance and should have discounted that race. There were 10 races in the series and nine count for points.
Had the Dunedin sailors deleted that race before the international jury hearing they would have won the silver medal. But it was too late after the hearing because the jury ruled it DNE (it could not be excluded).
Team manager Paul Meehan admitted "they were a bit naive. We didn't realise the repercussions. We should have withdrawn from the race".
Daniel Meehan (17), a pupil at Kings High School, was frustrated.
"We held second spot throughout the regatta," he said.
"After it was over we slipped back to fourth."
Meehan started competitive racing at the Waihola club when he was aged 10 and Morris (18), a pupil at Bayfield High School, started racing four years ago. He is the son of former New Zealand Noelex champion Neil Morris.
Morris will represent Otago at the New Zealand Starling championships at Auckland next month.
The pair have only raced together for the past nine months and this was their first international event.
"It was a great experience to race in a strong fleet like that," Daniel Meehan said.
"They are very sharp. We made mistakes but we will learn from that."
There was another factor of the regatta on the Sydney Harbour that surprised Meehan.
"There was a lot of traffic on the harbour and we had to dodge the ferry and big ships that sailed across our course," he said.
Meehan and Morris's race record at Sydney was: second, second, third, third, first, second, second, third, second, 16th. They finished fourth with 33 points, and were the third youth crew to finish.
The other Otago crew at the regatta was Chris Harris (16), of Bayfield, and Robere Hall (16), of Kings. They finished 11th overall, and seventh youth team.
In the Olympic 49er class, Peter Graham (24) and Rory Godman (20) finished 10th.
The event was won by James Campbell and Mark Asquith of Britain, with Australians Nathan Outteridge and Euan McNicol runners-up.
Outteridge, the current world champion, was fifth in the class at the Beijing Olympics.
The six Otago sailors are all members of the Ravensbourne Youth Yachting Trust, which helped fund their trip to Australia.
The trust was formed in 2000 with the help of Russell Coutts.
