After the home side dominated the opening 20 minutes, the first half ended on a quiet note with little goalmouth acton as the Millers best efforts came from two Adam Le Fondre shots from range.
Phil Jevons converted a Mark Duffy cross from close range 12 minutes after the restart to put the home team ahead.
Two minutes later Simon Hackney headed beyond Andy Warrington after Stewart Drummond crossed from the right unchallenged following a fast break down the right after a Rotherham corner.
Rotherham responded and striker Le Fondre drew three saves from Barry Roche, while Marcus Marshall headed straight at the Morecambe keeper.
The Millers deserved little from their afternoon by the sea however as the team left the field to boos from the visiting fans and calls for manager Ronnie Moore to be sacked after four successive defeats.