The Steamers started slowly but closed to trail 9-8 after a fine try to former Italy international Josh Sole set up by a superb tactical kick by young Australian fullback Elliott Hagan.
Just before halftime Steamers flanker Johan Bardoul got one back on the province that let him go by scoring a well taken try and with Willie Ripia's touchline conversion they went into the break ahead 15-12.
Playing into a freshening breeze, the Steamers played their best rugby of the season to put themselves in a seemingly unbeatable position. The forwards howed into their work with the aggression of the Steamers of old and the backline looked lively.
When outstanding winger Tino Nemani scored after a concerted attack the Steamers were in control leading 25-15.
But a succession of penalties conceded turned the tide in Waikato's favour and what hurt just as much was the unforced errors gifting possession away inside the Waikato 22.
Waikato forced the Steamers to clear the ball 24 metres out and from the lineout Waikato nailed their one clearcut chance of the second half.
It was no surprise the weak defensive channel between first and second-five eighth was targeted as it has been vulnerable all season. Waikato's Sam Christie broke through it and captain Jackson Willison won the game from the offload.
There was still time for one more Steamers raid into Waikato's red zone but another messy turnover ended last hopes.
The Steamers have one game left next Saturday against Northland in Whangarei before the soul searching and analysis will begin.
Waikato 28 (Jackson Willison try; Trent Renata con, 7 pens) defeated Bay of Plenty 25 (Josh Sole, Johan Bardoul, Tino Nemani tries; Willie Ripia 2 cons, 2 pens). Halftime 15-12 BOP.