Morgan (17), a pupil at Otago Boys High School, sprinted the last 400m lap in a blistering 63sec to win the combined men's and men's 17-19 title in 8min 42.50sec.
It was a personal best time by 9sec.
Morgan was followed home by 19-year-old Tony Payne (Caversham), who reduced his best time by 8sec to 8min 47.74sec.
Early pacesetter Ollie O'Sullivan (Hill City) was third in 8min 48.46sec.
O'Sullivan (21) was the only one of the five runners who broke the 9-minute barrier who is over the age of 20.
Caversham's Daniel Balchin (18) was fourth in 8min 49.12sec and Hill City's Campbell Garry (17) fifth in 8min 57.10sec.
Morgan typifies the teenage runners who are reaping the rewards for their big training miles.
He is a Lydiard-trained endurance athlete who has a tough weekly-training programme that includes two-hour runs, speed work at the Gardens, sprints at the Caledonian Ground, strength work up the Arthurs Walk steps and power-endurance work on the sand hills at Sandfly Bay.
The early pace was set by O'Sullivan who led through the first four laps at a steady 72sec for each 400m.
On the fifth lap, Payne jumped to the front and split the bunched field with a 65sec lap.
Morgan was the only runner who could stay with him but with two laps left he trailed by 2sec.
"Tony looked strong and I was worried," Morgan said.
"I found it tough and was struggling to stay there."
However, on the penultimate lap Payne started to falter and Morgan knew he had a chance.
He moved to the front just before the bell.
"I felt strong and confident.
"There was no point hesitating then," Morgan said.
He then sprinted home to win by 5sec to claim the men's aged 17-19 title.
O'Sullivan won the senior men's title.
Paula Whiting (Hill City) took the lead with two laps to go to win the women's title in a personal best time of 9min 54.27sec.
Kirsty Morris (Leith) also ran her best time when she finished runner-up in 10min 01.38sec.
The significant improvements came from Southland's Christina Taylor (16) who edged away from Hill City's Rebekah Greene (14) in the girls aged 15 and 16 race.
Both ran personal best times.
Taylor won in 10min 10.33sec and Greene reduced her time by 19sec to come second in 10min 11.77sec.
Greene broke four Otago records that have been held by Andrea Elvines (Alexandra) for the last 25 years in the girls aged 14,15, 16 and 17 grades.
Hill City's Myrtle Rough (68), the mother of New Zealand representative Shireen Crumpton, broke the New Zealand Masters aged 65 to 68 record by 36sec when she came third in the Masters women's over-35 event in 13min 48.73sec.
It was her third New Zealand Masters record in the age group.
She also holds the 1500m and 5000m records.
The other record came in the boys aged 13 4x100m relay when the Hill City team of Chris McNoe, George Woodhouse, Zakary Watt and Sam Watson ran 52.5sec.
The old record of 52.8sec was set by the North Otago team of Shane Scott, Richard Scott, Stuart Weir and Michael Shaw 32 years ago.
Thirteen-year-old Brent Cheshire (Ariki), who turns 14 this week, broke North Otago's Stuart Weir's 1976 boys aged 13 high jump record of 1.68m when he jumped 1.70m but it could not be claimed because of a technicality.
