Mangonui coach Mike Jurlina said it had been a good game but admitted the Bay remained a cut above their neighbours.
"Make no mistake, our boys put in a gutsy effort," Jurlina said. "We scrambled right up until kick-off to get the numbers due to injuries and non-availability, and prop Rodney Shepherd did a great job as captain.
"The players are looking forward to our home game and we should be a lot stronger for that one."
Mangonui try scorers were Rupeni Caucaunibuca, playing second-five and scoring from a great individual effort, wing Jarrod Albert and hooker Hazeley Windleborn.
The third and final round of the 2013 Harding Shield tournament will be played as a double-header at Arnold Rae Park on Saturday.
Harding Shield results:
Round 1: Whangarei 45, Mangonui 19; Rodney Northern Wairoa 36, Bay of Islands 19. Round 2: Whangarei 68, Rodney Northern Wairoa 17; Bay of Islands 45, Mangonui 17.