The Millers took the lead on the half hour when Stevenage failed to clear an Kari Arnason long throw. The ball was played back in by Arnason and Mark Bradley's shot went wide of Steve Arnold and found the back of the net.
Two goals in two minutes from Lee Frecklington then really put Rotherham in the driving seat.
The midfielder fired home from Ben Pringle's pass after 53 minutes and two minutes later he picked up a lose ball to plant a shot wide of Arnold.
But with the home side still celebrating Stevenage pulled one back with James Dunne firing home with a fine 30-yard effort after 58 minutes.
Stevenage grabbed a second after 72 minutes when Marcus Haber's shot was blocked and Filipe Morais fired home the lose ball but it was too little too late.