Although McClutchie appeared to lose the ball over the line referee Nick Briant awarded it and McClutchie added the extras.
Possession and territory was relatively even until McClutchie extended the lead with a handy penalty kick in the 16th minute after Briant ruled the Waikato frontrow had collapsed the scrum.
Waikato opened their account when winger Solomon Alaimalo celebrated his debut with a try which was converted by first five-eighth Rivez Reihana. The try followed an attack from the hosts through the backline and when the ball fell loose when Magpies winger Neria Fomai almost grabbed an intercept Waikato fullback Matty Lansdown was quick to pounce with a clever miss pass which put Alaimalo into space.
Hawke's Bay's defence was outstanding until Waikato centre Quinn Tupaea scored in the 39th minute. It came off a good flat pass from Reihana when the Magpies were down a player after winger Mason Emerson had been sinbinned for an early tackle.
Waikato led 14-10 at the interval. The fact the Magpies made 90 tackles in the first half, 75 more than Waikato, was an indication of how much the hosts dominated possession and territory during the second quarter.
Tupaea scored his second try in the 42nd minute. It followed good support play from the Waikato backs after a powerful scrum from the hosts.
The Magpies conceded 12 points while Emerson was in the bin.
Magpies halfback Folau Fakatava scored a crucial try in the 50th minute. It came after nine phases of pick and goes from the Hawke's Bay pack.
McClutchie converted and the visitors were back in the hunt. Hawke's Bay regained the lead with a try to prop Pouri Rakete-Stones in his blazer game after a drive from the Magpies pack in the 60th minute.
Waikato's engine room was down a player at that stage after lock Antonio Shalfoon had been sinbinned a minute earlier.
The Magpies had the bonus point for four tries when Emerson redeemed himself for his sinbinning with a try in the 65th minute to put the Bay ahead 27-19.
Waikato had a sniff of victory after replacement loosie Simon Parker dived over for the hosts bonus point try in the 72nd minute.
Match highlights
Heartstopper: The sinbinning of Magpies winger Mason Emerson in the 38th minute for an early tackle. Referee Nick Briant mentioned the possibility of a penalty try to his assistant referee but that wasn't warranted and fortunately for the Magpies not awarded.
Turning point: When referee Nick Briant blew the final whistle. The match could have gone either way until then.
Player of the match: Magpies first five-eighth Lincoln McClutchie. A cracker of a solo try even if it was debateable and sound game management from then on.
Scorers: Hawke's Bay 27 (Lincoln McClutchie, Folau Fakatava, Pouri Rakete-Stones, Mason Emerson tries; McClutchie pen, 2 cons), Waikato 24 (Quinn Tupaea 2, Solomon Alaimalo, Simon Parker tries; Rivez Reihana 2 cons). HT: Waikato 14-10.