After cruising with a 19 point lead with 14 minutes to go, Waikato hit the self-destruct button and very nearly replicated their last minute loss to Tasman last weekend.
Hooker Loni Uhila was shown a yellow card in the 66th minute and Counties scored two converted tries in his absence, before going close to scoring a Hail Mary, length of the field try with the final play of the game.
But Waikato did just enough for the win, and based on the full 80 minutes, it was a deserved one.
Three Waikato tries in the first 15 minutes stunned Counties, and the visitors were left with too much to do against a slick, hungry home outfit.
The bonus point win means Waikato keep pace with Auckland in fourth place and the first half performance will fill coach Johnny Walters with optimism heading into the second half of the season.
Waikato had to overcome the pre-match withdrawal of backs Jordan Payne (ill) and Declan O'Donnell (calf) but replacements Chauncy Edwardson and Regan Ware both put in impressive shifts and were heavily involved in the first three tries.
Fullback Wharenui Hawera also had an exceptional game, and his line break in the first minute where he fended, wrestled and stepped his way through five Counties defenders to set up the first try was one of the best runs of the season.
Counties finally showed what they are capable of with a slick backline break finished by Ashee Tuala in the 56th minute, but their renaissance begun just a little too late.
Waikato winger Joe Webber capped off a man of the match performance by scoring his hat trick in the 61st minute, showcasing his tremendous talent.
Waikato 26 (Joe Webber 3, Chauncy Edwardson tries, Damien Mckenzie 3 con), Counties Manukau 21 (Ahsee Tuala, Augustine Pulu 2 tries, Ahsee Tuala 3 con). Halftime - 19-0.
