Luton suffered a blow to their hopes of avoiding relegation after their three-match winning streak ended.
Reuben Reid beat Dean Brill from 12 yards to put Rotherham ahead before Drewe Broughton converted from a tight angle to make it 2-0.
Chris Martin's header reduced the deficit but Danny Harrison nodded home from 10 yards before Luton's Asa Hall made it 3-2 with a 25-yard strike.
But substitute Mark Hudson's late strike sealed victory for Rotherham.
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Luton: Brill, Keane, Pilkington, Bower, Emanuel (Parkin 79), Nicholls, Livermore, Hall, Martin, Craddock, Gallen. Subs Not Used: Davis, Henderson, Asafu-Adjaye, Jarvis.
Booked: Martin.
Goals: Martin 42, Hall 70.
Rotherham: Warrington, Tonge, Sharps, Fenton, Joseph, Danny Harrison, Reid, Mills, Jason Taylor, Burchill (Hudson 73), Broughton (Ryan Taylor 65). Subs Not Used: Cann, Nicholas, Clarke.
Booked: Mills, Sharps, Broughton.
Goals: Reid 11, Broughton 38, Danny Harrison 53, Hudson 87.
Att: 5,975
Ref: Darren Deadman (Cambridgeshire).
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