The Test great was the regular-season's leading run-scorer for a side that won only two games and finished last on the ladder.
The Thunder's next-most prolific batter Matthew Gilkes scored 201 runs fewer than the 433 Warner made in his eight digs.
Warner memorably smacked an unbeaten 130 runs against reigning champions Hobart in early January, the highest score recorded by a Thunder player.
It was one of two centuries Warner made this summer alongside his unbeaten 110 against the Sixers in the Sydney Smash last week.
Warner made his runs at league-high average of 86.6, scored more fours (38) than any other player and beat out Melbourne Stars skipper Marcus Stoinis for captaincy honours.
Stars paceman Haris Rauf led the bowling attack in the dream team after taking a tournament-high 20 wickets at 16.75.
Melbourne Renegades paceman Gurinder Sandhu, the tournament's second-top wicket-taker with 18, and rising Sixers allrounder Joel Davies were notable omissions from the XI.
Reigning champions Hobart were one of two teams without any players picked in the team of the tournament, despite being one of only three teams still in contention for the title.
The league's eight coaches, who vote on the team, also overlooked the Renegades.
The Stars, ousted from finals by the Hurricanes on Wednesday night, had a tournament-high five players selected including 41-year-old paceman Peter Siddle.
Perth Scorchers opener Finn Allen, newly-minted player of the tournament Sam Harper, former Test bat Matthew Renshaw and Sixers allrounder Jack Edwards were all selected in the team for the first time.
Adelaide Strikers quick Liam Scott was named 12th man as another first-time inclusion.
BBL TEAM OF THE TOURNAMENT:
Finn Allen (Scorchers), Sam Harper (wk, Stars), David Warner (capt, Thunder), Matthew Renshaw (Heat), Aaron Hardie (Scorchers), Marcus Stoinis (Stars), Jack Edwards (Sixers), Tom Curran (Stars), Haris Rauf (Stars), Lloyd Pope (Strikers), Peter Siddle (Stars), Liam Scott (12th man, Strikers).
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