The Millers would have been eyeing a first away win of the campaign against a team in the bottom three but they were sank by goals from Sammy Ameobi and Gary O'Neil at the University of Bolton Stadium.
Will Vaulks had levelled in the first half, but this was a damaging defeat for Paul Warne's men, who still have not won away at this level since April 2016.
Bolton went ahead in the 33rd minute when Ameobi sent a low shot across Marek Rodak and into the bottom corner.
But the Millers responded almost immediately as Vaulks headed home three minutes later.
Phil Parkinson's men won it after the break, though, when O'Neil converted after the Millers failed to clear a cross.
Bolton: Alnwick, Lowe, Wheater, Beevers, Taylor (Olkowski 67), O'Neil, Wilson, Williams, Ameobi (Buckley 90), Doidge, Donaldson (Magennis 78).Â Â
Subs: Vela, Noone, Hobbs, Matthews
Rotherham: Rodak, Vyner, Ajayi, Robertson, Mattock, Forde (Williams 66), Towell, Vaulks, Newell (Taylor 74), Smith, Proctor (Wiles 83).
Subs: Wood, Price, Manning, Raggett.Â
Referee: Jeremy Simpson