Hughes was disqualified after the race for entering too late.
Entries for the event closed an hour before the start, but Hughes and Ollie O'Sullivan (Hill City) were initially given late entries, issued handicaps and allowed to start.
Athletics Otago handicapper Richard Barker was asked by an Ariki official 10 minutes before the race started to give Hughes a handicap.
"I'm not responsible to say whether a guy should run or not," Barker said.
"That's up to the officials.
"In terms of the laws, they were properly entitled to disqualify Kane."
That decision was taken by the meeting manager Ron Cain.
The decision was passed on to Hughes by the president of Athletics Otago Brent Halley.
"The entries closed an hour before the race and Kane entered just before the start," Halley said.
Hughes (18) was naturally disappointed to be disqualified after running such a strong race.
But he understood the officials' reasons.
Earlier this year, he won the junior men's Port Chalmers to Dunedin handicap road race and he won the Sir James Barnes handicap cross-country two years ago.
Helm (44), a Dunedin accountant, pleaded with officials not to change the result.
"I feel a bit guilty," he said.
"But I guess the officials had to stick to the rules."
Helm wanted Hughes to share in the celebrations and they held the cup together at the victory presentation.
The win was a milestone for Helm who became only the fourth runner to win the event more than once since it was first held in 1935.
He also won in 1998.
Martin Mackinnon (Civil Service) won in 1943-44, Keith Darling (University) in 1965-66 and 1972 and Phil Morris (Hill City) 1986 and 1997.
Hughes, running off a handicap of 1min 20sec from the start, was sixth at the bell and made his move down the back straight when he closed on the leaders.
He went into the lead around the final bend and was chased into the straight by Helm.
Helm, who was running off the 1min 25sec mark, attacked 80m out but Hughes fought back.
"I felt good and knew I could sprint," Hughes said.
Helm made a second bid 60m out but felt flat.
"I hit the wall when I tried to go a second time," he said.
Helm finished in a time of 5min 15.20sec and Hughes was just four seconds behind him.
Fastest time went to scratch man Glen Ballam (Southland) in 4min 29.65sec.
The highlight in the other events was the men's discus that was won by national senior champion Michael Hall (Taieri) with a throw of 46.12m.
Club mate Kieran Fowler was second with 44.85m.
William Hubber (Taieri) won the junior men's discus with 40.47m and the hammer throw with 47.21m.
Southland athletes dominated the women's jumps with Charlotte Muschamp winning the high jump with 1.7m and Greer Alsop the long jump with a leap of 5.24m.
There was a dead-heat in the men's high jump with Elton Matternich (Southland) and Brent Cheshire (Ariki) both clearing 1.8m.
It was a personal best jump for Cheshire by 10cm.
There were three Otago records, with the most significant being the girls aged 15 400m by Rebekah Greene (Hill City) who broke the record run by Kirstin Downie (Leith) in 1984 with a time of 58.12sec.
Meg McKay (Hill City) set a new mark in the girls aged 13 high jump with a leap of 1.57m that beat the jump of Genevieve Sullivan (Hill City) in 1982.
Jim Flynn (Leith) broke his fourth Otago record in the last four weeks in the men's aged 75 to 79 5000m with a time of 27min 30.53sec.
A week earlier he set a new mark in the 10,000m with a time of 59min 35.43sec.
He also holds the 1500m and 3000m records.
