Racing in blustery conditions, he was never going to get close to his national record (7min 36.91sec).
But the middle distance star crossed the line in 8min 0.09sec, well clear of second-placed Hamish Carson, who clocked 8min 5.97sec.
Willis sat back in eighth place for most of the race, and was seventh with two laps to go.
But he made his move in the penultimate lap, quickly joining leader Malcolm Hicks and Carson at the front.
He bolted past the pair with about 500m to go and opened up a good lead with a lap to run, cruising to the line for the comfortable win.
Julian Matthews, of Tasman, made a late move to pip Hicks on the line and finish third in 8min 7.40sec.
Otago's Caden Shields, of Hill City-University, finished 13th in a personal-best 8min 35.71sec, while Joshua Baan, of Caversham, was 15th in 8min 40.51sec.
In the women's race, Canterbury's Rosa Flanagan won a thriller in 9min 9.33sec. She had Lucy Oliver, of North Harbour, hot on her heels with a lap to go, but managed to hold off her challenge.
Oliver crossed the line in 9min 10.67sec to finish second, while Lydia O'Donnell, of North Harbour, passed Camille Buscomb over the last 200m to finish third in 9min 14.99sec.
Otago's Hanna English finished 11th in 10min 21.05sec.
The 3000m championship races were held as part of the annual Capital Classic and a bunch of other Otago athletes headed to Wellington.
Andrew Whyte, of Hill City-University, was most impressive.
He won the 400m in 47.54sec, a solid win in tough conditions. Frazer Wickes, of North Harbour, was second in 47.89sec.
Other top-five performances included. -
● Felix McDonald, of Taieri, finished third in the men's 110m hurdles (15.07sec).
● Christina Ashton, of Taieri, finished fifth in the women's 100m hurdles (14.83sec).
● Sammy Burke, of Aspiring, finished fifth in the junior women's 1500m (4min 50.33sec).
