The hosts climbed back into the contest with tries from Joe Webber and Leroy Carter, only for a missed conversion from Lucas Cashmore leaving them a point in arrears.
Waikato built on that lead in the 70th minute through Rupeni Tamani's try, before a couple of expert kicks from D'Angelo Leuila made the game safe.
The sixth-placed Bay of Plenty won't have long to recover as they continue in their quest for a top-four bid, completing a busy final stretch with games against Northland on Wednesday and Canterbury on Saturday.
Waikato meanwhile are unable to catch Hawke's Bay atop the Premiership standings, with the Magpies solidifying their front-running status with a 40-31 victory over Manawatu tonight.
But the competition leaders were as severely tested as they have been all season in Palmerston North.
The visitors, who had already wrapped up top spot, found themselves in a 24-12 hole with half an hour to play after Nehe Milner-Skudder scored Manawatu's third try.
But what had been a stout defensive effort from the Turbos was quickly blown away as Hawke's Bay poured on 28 points in 22 minutes.
The carnage started when Ollie Sapsford completed his hat-trick following a first-half brace, with a double from Kienan Higgins eventually sealing the Magpies' seventh win from eight games this season.
Manawatu stayed in second spot in the Championship, where the final playoff place remained up for grabs after Southland ended a year of pain with a 37-33 win over Northland in Invercargill.
The Stags hadn't enjoyed an NPC victory since November 5 last year but, due to the Covid-disrupted nature of this year's competition, their narrow triumph kept them in the semifinal hunt.
Northland are currently in fourth with 10 points, one ahead of Southland, with the inactive North Harbour and Counties Manukau leaving five teams to fit into four spots.
Bay of Plenty 33 (L Cashmore, N Harris, J Webber, L Carter, E Narawa tries; L Cashmore 4 con)
Waikato 37(C Ratima 2, M Dawai, R Tamani tries; D Leuila 4 con, 3 pen)
Halftime: 14-20
Manawatu 31 (S Hurley-Langton, L Mitchell, N Milner-Skudder 2 tries; B Cameron 3 cons, pen, S Cruden)
Hawke's Bay 40 (O Sapsford 3, P Rakete-Stones, K Higgins 2 tries; L McClutchie con, C Makene 4 cons)
Halftime: 17-12
Southland 37 (J Moorby, S Alaimalo, M James, G Pleasants-Tate tries; M Banks 3 pens, 4 cons)
Northland 33 (P Leilua, D Hawkins, R Ranger, J Macilai-Tori tries; D Hawkins 3 pens, 2 cons)
Halftime: 23-15