The visitors weren't helped when all three officials missed a forward pass which led to the hosts first try in the seventh minute to winger Iliesa Ratuva.
Hawke's Bay finished the game with 25 missed tackles, 13 more than Waikato.
The Magpies were still in the game until Ratuva scored his second try with 11 minutes remaining to give the hosts a 39-22 lead.
The Magpies Bath-bound centre Robbie Fruean is likely to miss the Bay of Plenty game with a hamstring injury.
Scorers:
Waikato 46 (Iliesa Ratuva 2, Jordan Trainor, Willis Halaholo, Tau Koloamatangi, Jason Robertson tries; Trainor 5 cons, 2 pens), Hawke's Bay 22 (Tony Lamborn, Mason Emerson, penalty try; tries; Ihaia West 2 cons, pen). HT: 27-3.