The Millers totally dominated the first 45 minutes and deservedly took the lead after 30 minutes, but the easiest chance of the half fell to the visitors.
The home side had two efforts cleared off the line by Anthony Grant, and Ian Sharps and Kari Arnason went close with headers, but Boro should have grabbed the lead after 13 minutes.
Filipe Morais picked out Marcus Haber on the penalty spot but with only the keeper to beat he shot straight at Andy Warrington and the keeper saved with his legs.
Rotherham took the lead on the half hour when Stevenage failed to clear an 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 deflected 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 Maber's shot was blocked and Morais fired home the lose ball but it was too little too late.
Source: PA
Source: PA