It was the fourth win in five games for Wellington whose young side of homegrown talent showed glimpses of the potential that could see them go all the way in the competition.
Waikato made a dominant start and although Trent Renata missed his first two penalty goals, he nailed his third to open up a three point lead.
On a typical windy Wellington day he wasn't the only one struggling with the conditions - Lions fullback Jason Woodward was also unsuccessful from two regulation penalties -and after 18 minutes there had only been one successful kick from five attempts.
Finally Wellington sprung to life in the 20th minute with a passage of great offloads and good direct running leading to Eric Sione's first ever ITM Cup try.
Waikato had beaten Bay of Plenty 15-6 on Tuesday and the fallout from the quick turn around looked ominous, as the visitors started falling off tackles late in the first half, with fatigue looking the most likely explanation.
Ardi Savea made Waikato pay for a horrible error just before halftime when Tawera Kerr-Barlow's weak attempt at a left footed chip kick was intercepted and bundled over the line.
Waikato constructed an unstoppable rolling maul to get big replacement prop Ted Tauroa over the line after the break, but Wellington struck back just as quickly when Shaun Treeby was the benefactor of a stylish Dane Coles one-handed pickup and release.
Wellington then fought off a spirited Waikato attack through the last ten minutes - including a controversial disallowed try - to maintain their 11 point lead before Woodward picked up their bonus point try with the last action of the match.
Wellington 29 (E Sione, A Savea, S Treeby, J Woodward tries; J Woodward 3 con, pen) Waikato 13 (T Tauroa try; T Renata con, 2 pen) Halftime 14-6.
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