The Wolves went into the clash with no chance of reaching the play-offs after Catalans' surprise win at St Helens on Friday.
Harlequins, who led 16-10 at one stage, have now won only one of their past 12 games to plunge from fourth to 11th.
Warrington were without five of their Wembley-winning side with Chris Hicks, Matt King, Paul Johnson and the Anderson brothers, Louis and Vinnie, missing out.
The Wolves handed a debut to teenage hooker Alex Thompson on the bench and he celebrated with a second-half try after a surging Garreth Carvell break.
But it was a typical end-of-season show with both sides making a litany of errors.
Warrington could not have made a worse start with man-of-the-match Lee Briers booting the kick off straight into touch and Quins taking only 80 seconds to go ahead with Tony Clubb scoring from Danny Orr's cross-field kick.
Quins, who thrashed Warrington 60-8 in March, made it 10-0 when Dorn shot through and Matt Gafa converted.
The Wolves finally opened their account midway through the first half with a sizzling try after Matty Blythe's surging break was eventually finished off by Kevin Penny.
Warrington levelled when Ben Westwood cut inside Jamie O'Callaghan from Michael Monaghan's pass for Chris Bridge to convert.
But Lee Mitchell's mistake and sloppy tackling allowed Dorn to spin over for his second try with Chris Melling's conversion making it 16-10.
Quins were reduced to 12 men when Australian Luke Williamson was sin-binned just before the break for holding down Chris Bridge and Briers waltzed over to make it 16-16 at half-time.
Quins were still a man short when Blythe scythed through from Briers pass to fire Warrington ahead for the first time.
Carvell then created Thompson's touchdown before Penny added a second try to stretch the lead to 32-16.
O'Callaghan and Matt Gafa crossed for Quins to cut the gap to 32-28.
Mickey Higham and Dorn, who completed his hat-trick, traded tries before Tyrone McCarthy settled the issue.
Warrington paraded the Challenge Cup in front of their fans after the final hooter but their final Super League placing will be a big disappointment.
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