Godfrey, who is from Dunedin club Neptune, recorded wins in the senior 200m and 400m individual medley to help the Makos finish with 840 points.
The zonal championships put 160 of New Zealand's leading and up-and-coming swimmers against each other in a collegiate-styled competition.
Swimmers from all regions in the country are divided into four zones, with the Makos comprising South Island swimmers. Each team is made up of 10 male and 10 female swimmers in both the senior (16 and over) and junior (under-16) competitions.
Otago had 11 swimmers - Andrew Trembath, Godfrey, Caitlin Deans, Cecilia Crooks, Olivia Gold, Devon Familton, Jordan Rahurahu, Jeremy Tasker, Kou Kitahara, Gabrielle Trotter and Mila Jojic - picked in the Makos.
Swimmers earned from 26 points (win) to four points (eighth place) in each race, while each zone could designate four joker swimmers, who earned double points.
Trembath had a couple of good individual performances in the senior section, finishing second in the 100m backstroke and third in the men's 200m individual medley. He also swam some strong relay legs.
The Harlequins, from Northland, Auckland and Counties-Manukau regions, a team that boasted junior world champion Gabrielle Fa'amausili, dominated the night to finish on 1091 points.
The All Stars were third in the senior competition with 718 points, while the AquaKnights were fourth on 698.
In the junior section, the Harlequins also came out on top (967), ahead of the AquaKnights (855), All Stars (751) and Makos (731).
The championships concluded with swimmers taking part in a 1000m freestyle relay for all swimmers in the senior and junior divisions. The Harlequins steamed home ahead of their competitors in both.
