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.
Disrupted by suspensions, 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Thomas got himself in several first-half altercations and was withdrawn by Rotherham boss Steve Evans at half-time.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.