The Steamers lifted their defensive intensity and set about softening up the Wellington forwards with some big hits and old-fashioned footwork in the rucks.
A defining moment in the game came in the 20th minute.
It stemmed from another Steamers handling error, after they looked sure to add to their try tally for the night with some well structured phase play. Wellington bravely ran the loose ball out in front of their posts and after a speculative pass hit the goal post pad, they roared down the field, with classic inter-passing between backs and forwards.
Finally, it was winger Alipate Leiua who finished off one of the tries of the season.
The Steamers' injury woes continued with Kefu, and what looked a serious leg injury to lineout champion Culum Retallick.
Noakes missed two penalty attempts before he landed two, to close the deficit to 20-16, but Sopoaga stretched the lead to 23-16 at halftime.
Steamers coach Kevin Schuler wanted more urgency from his forwards in the second half but his team got off to a muddled start, struggling against the wind.
Wellington won a rare tighthead in the Bay's 22 and profited from dithering defence to score a sharp try to second-five Shaun Treeby. Sopoaga converted and the Bay had a mountain to climb at 30-16 down.
A brilliant 40-metre break by Lelia Masaga sparked the Steamers into life and after 10 phases on attack, they won a penalty. From the lineout option, the forwards piled into their work and the man who started it, Masaga, dived over.
Noakes converted and then landed a wide-angled penalty as the Steamers began to dominate territory. Though Sopoaga then kicked another penalty to move the Lions ahead 33-26.
A Phil Burleigh break looked promising with 15 minutes to play but Noakes spilled the crucial pass with plenty of players in support. The Steamers had another great chance with Wellington stretched but the scoring pass was intercepted by Tim Bateman.
The final stages were frantic as a desperate Bay team looked for a way through, but their poor handling scuppered more opportunities.
Wellington pushed the Steamers off their own scrum feed to win a late penalty and three points from Sopoaga to move his team out to a 10-point lead. Replacement Nick McCashin ended an average goal kicking night for the Steamers, when he missed a chance to gain the Steamers a bonus point.
And that may well have been the death blow to the Steamers' semifinal aspirations.
Wellington 36 (Ross Filipo, Alipate Leiua, Shaun Treeby tries; Lima Sopoaga 3 cons, 5 pens)
Bay of Plenty 26 (Mafi Kefu, Lelia Masaga tries; Chris Noakes 2 cons, 4 pens)