Waikato skipper Dwayne Sweeney regained the lead for Waikato with a 25th minute penalty, only for Taranaki to storm back with two tries in the shadow of half- time.
The first was set up by Te Toiroa Tahuriorangi's acceleration and quick hands; the speedy halfback making the initial break then offloading for Charlie Ngatai to score between the uprights.
The second came two minutes later, first five-eighth Stephen Perofeta showing impressive speed down the left touch to build a 19-10 lead for the hosts.
Taranaki looked well in control when centre Sean Wainui dotted down out wide to extend the lead five minutes after the restart, but Manihera's quick tap from a scrum penalty caught them napping.
Tries to Seta Tamanivalu and Beaudein Waaka restored Taranaki's margin, but their comfortable 34-15 lead at the 63-minute mark evaporated thanks to two more Manihera tries, bringing up his hat-trick.
However, Taranaki's defence held firm in steadily increasing rain to close out a hard-earned victory.
Elsewhere, Hawke's Bay have avoided a season-opening upset in the Mitre 10 Cup, mounting a comeback to overcome Southland 24-16.
Hawke's Bay didn't win a single home game last season and were relegated from the Premiership as a result, and their return to the Championship had some early struggles.
Southland, who came into the game as heavy underdogs, led 13-3 after 48 minutes, but Hawke's Bay eventually found their footing, overcoming a yellow card and a slew of injuries to eventually bank a hard-fought victory.
For the hosts, winger Mason Emerson suffered a leg injury and flanker Tony Lamborn went off with an arm injury. Number eight Gareth Evans increased the infirmary patient register to three before halftime, traipsing off the park with a thigh injury.
The injuries left Hawke's Bay with an uphill task in the second half, but in a span of ten minutes, the game changed.
First, TJ Vaega finished off a flowing move, started by his brother Cardiff, and while Southland hit back with another penalty, Hawke's Bay took their first lead of the game when promising youngster Tiaan Falcon was the first to a kick through to dot down.
The hosts were briefly reduced to 14 when Geoff Cridge was sent to the bin for a poor tackle, but Southland couldn't capitalise, and the Bay capped off their come-from-behind victory when Marino Mikaele-Tu'u barged over from close range to secure the win.