The 27-year-old striker, who arrived on loan from Bury on Wednesday, charged down Bilel Mohsni’s attempted clearance and netted from just inside the box to put the Shrimpers in front with only nine minutes gone.
Southend thought they had equalised two minutes later but Elliot Benyon’s header was ruled out for offside despite the ball appearing to have been played by a Rotherham player.
Harrad might have had a second but his header was well saved by Glenn Morris, while Rotherham goalkeeper Rhys Taylor pulled off a one-handed save to deny Ryan Hall before getting a foot to block another effort from the winger.
Southend boss Paul Sturrock brought on strikers Neil Harris and Jack Sampson to try to force a goal but former Southend striker Alex Revell made the points safe for Rotherham in the 83rd minute with a 20-yard shot that went in off the post.
The win ended a run of three straight defeats for Rotherham, while Southend missed the chance to go top of League Two.