Henderson (38), a Dunedin car salesman, came with a rush over the last of the six laps to win the prestigious 1500m handicap event at the Mosgiel velodrome.
Henderson was off a handicap of 100m and he was followed home by Mark Falcous (150m) and Katherine Jones.
Greg Henderson, the former international and now a professional road rider, won the event in 2002.
He now lives in Melbourne.
"It's special for me," Chris Henderson said.
"I was pleased to join Greg because the race is the special event on the track in Otago each year.
"I will get a photo of myself holding the cup and send a copy to Greg."
It was a special win for Henderson, who only returned to cycling four years.
He had ridden as a novice, but work and family commitments took over and there was an 18-year gap, he said.
He has made up for lost time by winning bronze medals in the veterans 500m derby at the New Zealand championships in 2008 and 2010.
Henderson is noted for being quick off the mark in a standing start and used this ability on Saturday night.
"I got a flier and caught the group in front of me in the first lap," he said.
He was helped by Neil Derbyshire, who took the pace on the penultimate lap.
Defending champion Mark Spessot started 50m behind Henderson but was not able to bridge the gap.
The annual race was first held in the 1950s as part of Dunedin's Festival Week and is one of the prestige events on Otago Cycling's summer Calendar.
Meanwhile, Phil Turnwold claimed victory in an exciting James Faulding Memorial Handicap road race yesterday.
Turnwold turned up the heat on the final sprint to cross the line ahead of Brendon Hastie and Kev Thomson.
Dave Headley held on to fourth, with Kat Jones finishing fifth and first woman home.
Spessot brought in the scratch group to claim fastest time honours.
In the junior race, Denton Hayward was first and had the fastest time, with Joshua Carpenter and Caleb Hope in second and third place respectively.
- Additional reporting by Steve Havard.
