WGHS fought hard and clawed one back through Emma Illerbrun just before halftime of the Friday night match.
The school side then used their pace and put Maungakaramea under a lot of pressure in the third quarter but Thomson was praised the way the Maungakaramea defence held strong.
"Huge kudos to our defence, as there were some periods of play where Girls High almost got on top of us, but we were able to regain control after some great defensive efforts," Thomson said.
With five minutes to go Maungakaramea sealed the win when Morgan Forrester converted a sideline attack.
"We are all very happy with how we played, and it was great to come out with the win as Girls High are always a fast and skilful team to come up against," Thomson said.
In the other premier women's match played on Saturday, Springfield beat Hikurangi 3-0.
In the premier men's competition, Whangārei Boys High School turned the tables on their first-round defeat to beat Mangapai 2-0 while Springfield converted an early chance and held on to beat Bream Bay 1-0.