Magpies second five-eighth Pasqalle Dunn was in the sinbin for a dangerous tackle when his Waikato opposite, captain Dwayne Sweeney, scored in the 18th minute. First five-eighth Fletcher Smith slotted the conversion.
Magpies first five-eighth Tiaan Falcon put the visitors back in front with a handy penalty in the 22nd minute.
Waikato took a 14-10 lead when winger Sevu Reece captialised on a lucky bounce at lineout time. Smith was again on target.
Reece set up No 8 Jordan Manihera for his try in the 32nd minute which Smith converted. This followed Magpies flanker Marino Mikaele-Tu'u, who earnt his blazer for 1000 minutes, being penalised for not wearing his mouthguard.
Four minutes later Magpies lock Tom Parsons, who was in the Magpies 2014 shield winning side, scored from a lineout move. Waikato led 21-15 at halftime.
Soft turnovers proved costly for the Magpies in the third quarter. Reece was again involved in the buildup before Waikato's substitute loosie Murray Iti scored in the 59th minute. Smith again converted.
Smith scored a clever solo try in the 66th minute which he converted to give the hosts a 35-15 lead. Superb support play from Waikato saw halback Raniera Takarangi score in the 71st minute. Smith maintained his 100 per cent success rate with his sixth conversion.
To their credit the Magpies didn't chuck the towel in and were rewarded with a 78th minute try from substitute back Sasa Tofilau. Utility back Stacey Ili converted.
Discipline lapses proved costly for the Magpies in the first half. This allowed Waikato to enjoy 65 per cent of the territory and 55 per cent of possession during the first 40.
Sweeney had every right to be proud of the manner the hosts handled their third outing in eight days.
"Noone would have thought we had played three games in eight days when we finished like that."
While promising Waikato centre Quinn Tupaea got the player-of-the-match award it could have easily gone to Smith or Reece.
None of the Magpies would have been proud of their second half effort. Their numerous discipline lapses are unacceptable at this level.
As a Highlanders and 2017 world champion Baby Black Mikaele-Tu'u should know better when it comes to keeping one's mouthguard in.
With their chances of winning the Ranfurly Shield dashed the Magpies must focus on earning a semifinal berth. They have enough ammunition to do that provide they fix up their missed tackle count, discipline lapses and soft turnovers conceded count.
Waikato's next shield defence will be against Southland in Hamilton on September 29. The Magpies have plenty of time to regroup before hosting North Harbour on September 22.
Match highlights:
Heartstopper: Magpies second five-eighth Pasqualle Dunn being sinbinned in the 11th minute for a dangerous tackle. Waikato scored seven points while he was on the sideline.
Turning point: When Waikato's substitute loosie Murray Iti scored and first five-eighth Fletcher Smith converted in the 59th minute to give the hosts a 28-15 lead.
Player of the match: Waikato centre Quinn Tupaea. Poerful on the carry and plenty of clever offloads. Only just ahead of Smith.
Scorers: Hawke's Bay Magpies 22 (Brad Weber, Tom Parsons, Sasa Tofilau tries; JJ Taulagi con; Tiaan Falcon pen; Stacey Ili con), Waikato 42 (Dwayne Sweeney, Sevu Reece, Jodan Manihera, Murray Iti, Fletcher Smith, Raniera Takarangi tries; Smith 6 cons). HT: Waikato 21-15.
