The Robins, who twice made unsuccessful bids to sign Thomas in this season's transfer windows, fell behind after only 58 seconds when the journeyman striker latched on to a pass from the influential Ben Pringle to give Rotherham the lead.
Swindon struggled to find any rhythm and Rotherham twice missed good chances before Thomas doubled the visitors' lead with a far post 23rd minute header, again set up by Pringle.
Thomas got himself in several first-half altercations and was withdrawn by Rotherham boss Steve Evans at half-time.
Michael Smith twice wasted early second-half headers for Swindon before reducing deficit from the penalty spot after Australia World Cup hopeful Massimo Luongo was fouled.
The 60th-minute goal sparked Swindon into action and Jay McEveley thundered a 30-yard left-foot shot against the bar. But that was as good as it got for the hosts as the Millers move on to the play-offs.