A snowstorm during the half-time interval proved a bigger threat to the Black Cats collecting three points and closing the gap on the top two in the chase for automatic promotion.
Thornton, on for the influential Julio Arca after just half an hour, scored two cracking goals from 25-yard free-kicks, but goalkeeper Mike Pollitt gifted the Black Cats the other two goals.
Andy Monkhouse pulled a goal back in the 77th minute with a sweetly struck low drive, but it was much too little, too late to stop the home side's push for promotion.
Despite Rotherham making a bright start, forcing four corners in the first six minutes, they were rarely seen as an attacking force as the home side gradually took control.
After Stephen Elliott had fired straight at Pollitt, the keeper gifted the Black Cats the softest of goals in the 13th minute. Arca linked up with George McCartney down the left flank and the ball was moved on for Marcus Stewart to centre.
Dean Whitehead's header should have been a routine save for Pollitt, only for the keeper to allow the ball to slip through from his grasp and through his legs.
Elliott was guilty of missing a sitter before Thornton increased the lead in the 35th minute after Jamal Campbell-Ryce had handled.
Stephen Wright rattled the top of the bar immediately after the break but from Thornton's corner, Gary Breen's downward header again went through Pollitt's legs.
Pollitt partially redeemed himself with fine saves from Thornton and McCartney, but was again well beaten from a Thornton free-kick in the 73rd minute.
To their credit the Millers stuck to their task and Monkhouse's well-taken goal was just reward for their spirited efforts.