The 5.7-magnitude quake affected the Christchurch area about 10 minutes before the 18-year-old began play.
But she started her round on time and finished with a two-under 70.
Ko won on 10 under, two shots clear of England's Felicity Johnson, South Korean amateur Hye-Jin Choi and Denmark's Nanna Koerstz Madsen.
"It was lucky I wasn't out there playing because I wouldn't want to be in the middle of my swing and the ball moves somewhere else," said the teenager afterwards.
"It's been a long week, a lot of emotion and a lot of people to share this amazing victory with. Especially given how much New Zealand golf has been a support to me and my career."
Ko's success follows her victories in the event in 2013 and 2015.
Home favourite and world number one Lydia Ko shrugged off the effects of an earthquake to win her third New Zealand Women's Open title in four years.