Fresh off arriving at the ground by helicopter from his brother's wedding, Warner won his personal battle with long-time Test teammate Steve Smith but still tasted defeat in front of 41,027 fans on Friday night.
Chasing 152 for victory, the retired Test opener hit 37 from 39 balls on a slow SCG wicket but had no support as the Thunder were all out for 132 in the final over.
While Warner was the retiring hero at the SCG last week, veteran Sixers spinner Steve O'Keefe took 3-13 in his last home regular-season match.
The result officially ends the Thunder's slim finals hopes, and locks the Sixers in for another post-season appearance.
A win in Perth on Tuesday night will allow the Sixers to finish runner-up on the ladder and earn a second chance, otherwise a home elimination final awaits.
The Sixers win came despite Smith being caught on the first ball of the game, in his final appearance for the club this summer.
The Sixers got off to the worst-possible start with a golden duck for opener Steve Smith. (Steve Markham/AAP PHOTOS)
A century-maker in the same fixture last year, Smith hooked a short Daniel Sams ball straight to Nathan McAndrew at deep-backward square.
The golden duck came in Smith's first game since being appointed Warner's replacement as Test opener.
In Smith's absence, his young lookalike Josh Philippe took charge of the Sixers' innings with a well-timed 47 from 35 balls.
Philippe scooped Sams for four late in the first over and played well square of the wicket.
Jordan Silk struck 35 to help the Sixers to 7-151, as the Thunder's spinners dominated and Tanveer Sangha took 2-22 from his four overs.
In reply, the Thunder looked on track early when Warner and Alex Hales took 44 runs from the opening four-over powerplay.
Warner pulled Sean Abbott for a six and drove Jack Edwards for another as he went aerial early, to be 15 from six balls at one stage.
But when Hales was bowled by O'Keefe for 28, the air went out of the Thunder's innings.
Cameron Bancroft's rough week continued when he was beaten in flight and bowled for two by O'Keefe, while Warner's last 22 runs took 33 balls.
David Warner's helicopter touched down at the SCG ahead of Friday's Sixers-Thunder BBL clash. (Steve Markham/AAP PHOTOS)
And while the veteran opener batted through to the 17th over, he was eventually the seventh man out when caught in the deep by O'Keefe.
It summed up the Thunder's night, as their season's hopes ended with a final 16 overs at the SCG where they scored 10-88.
After starting the evening landing in a chopper with his Thunder playing hat on, Warner is now staring down the barrel of two dead rubbers to finish a club season that never really took flight.
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