The Blues earned a consolation win late in the season defeating Western Force 32-9 at Eden Park.
Steven Luatua, Charles Piutau Ma'a Nonu and Luke Braid scored the Blues' tries with Lachie Munro kicking 12 points.
Force's points came from the boot of Ben Seymour.
The Lions gave themselves hope of avoiding the wooden spoon with a 37-32 win over the Melbourne Rebels in Johannesburg.
Johan Ackermann's side snatched the win when Elton Jantjies landed a touchline conversion after replacement Jaco Kriel's 74th-minute try had drawn them level. Jantjies also added a last-gasp penalty.
Elsewhere, the Stormers retained the South African Super Rugby conference title with a 13-6 victory over the Cheetahs in heavy rain at Bloemfontein.
Gio Aplon scored the only try of the match for the Stormers, who missed out on the bonus point which would have taken them above the Chiefs in the Super 15 standings.
Peter Grant kicked six points for the victors, who were level at 3-3 at the break, while the Cheetahs' only points came courtesy of two penalties from Riaan Smit.
The Brumbies edged out the Waratahs 19-15 at ANZ Stadium.