Whyte (21) was quick off the mark after the Town Hall clock rang out the first of its 10 chimes at 10am, before finishing the 243m run around the Octagon in 32.59sec.
He crossed the finish line - outside the New Zealand Shop - just as the 10th and final chime was finishing.
So close was the finish, Whyte did not think he had beaten the clock immediately after the race.
Whyte, the Otago 400m record-holder (46.25sec) and holder of the fifth-fastest 400m time in New Zealand history, pocketed $300 for winning the race and another $250 for beating the clock.
However, he fell 1.04sec short of beating Cory Innes' 2008 record (31.63sec), a feat which would have added another $500 to his winnings.
Whyte, who was running the event for the first time, said he was not thinking about the chimes and he just ''got out and ran''.
''I wasn't really counting the chimes. I sort of got to the front quite easy, then took it easy down hill, then came home strong,'' he said.
The $550 he won will help the University of Otago finance and competition modelling student finance his busy season.
Whyte, a member of the national 4x400m relay team attempting to qualify for the world championships, will compete in Hobart, Canberra and Sydney over the next month, before the national and Australian championships in March.
Felix McDonald (16), the top-ranked 300m hurdler in his age-group in the country, pushed Whyte all the way and finished second in 33.88sec.
Jarrod Adams ran the race before getting married in Dunedin in the afternoon and was cheered on by friends and family. He finished sixth in the men's race in 37.78sec.
Christina Ashton, one of the best short hurdlers in the country, bolted home to win the women's race in 38.82sec.
Ashton fended off a strong challenge from sprinter Caitlyn George (39.58sec) to claim the $300 prize.
Madaline Spence was third in 40.07sec, while 50-year-old Liz Wilson was fourth in 40.75sec.
Innes (2008), Andrew Moore and Toby Flett (both 2009) are the other runners to have beaten the clock in the race restricted to six men and six women.
by Robert van Royen
