The Millers inflicted a seventh successive defeat on the hosts.
The first chance went to the visitors as a Lionel Ainsworth cross found new loan signing Lee Frecklington, who scuffed his shot straight at Shots 'keeper Jamie Young.
Rotherham took the lead after 34 minutes when Frecklington pounced on a weak clearance to fire into the top corner from 20 yards on his debut - setting Steve Evans' side on their way to a first away win of the season.
Rotherham continued to boss proceedings after the break, Ainsworth testing Young - who kept the score down - with two low drives and Frecklington also going close in a dominant five-minute period for the Millers. And they were rewarded in the 56th minute when Troy Brown was penalised for bringing down Frecklington and Bob Harris bent home a 25-yard free-kick.
Alex Revell then rounded off the victory with a late tap-in as Young could only push Ainsworth's 25-yard drive into the striker's path.
Shots top scorer Craig Reid registered the hosts' first shot on target after 83 minutes - to ironic cheers from the home terraces.