Stevenage had the better of the first half but did not open the scoring until a minute before the interval when Peter Winn smashed home a low shot past Andy Warrington from 20 yards.
Stevenage went on to dominate as David Bridges planted a free header over the crossbar and Chris Beardsley nodded wide from six yards.
Adam Le Fondre went close for Rotherham with the first chance of the second half, but the hosts responded with Michael Bostwick powering in a 20-yard drive which flew narrowly wide.
Stevenage all but wrapped up victory with five minutes remaining when Rob Sinclair crossed low and Byron Harrison guided home a shot from eight yards.
Scott Laird wrapped up a convincing win when he crashed home an unstoppable shot in stoppage time.