Set piece, particularly lineout, floundered on occasions in handy positions as Northland searched for more tries but the Mooloos scrambled well in defence.
The visitors had two tries disallowed and once knocked the ball on, on the tryline in slippery conditions on a drizzly evening at Semenoff Stadium.
Just as the Taniwha started strongly in the opening half, Waikato touched down five minutes after the breather through hooker Rhys Marshall who took a quick tap after Northland halfback Sam Nock was penalised for holding on to the ball in front of the posts.
Injured All Black Jack Goodhue took the field in the 50th minute for Northland and had he held on to the ball in Waikato's 22 with time almost up, and a vocal crowd getting behind their team, the final result may have been different.
Northland's next match is against Wellington in Porirua next weekend.