Rotherham debutant Shaun Harrad scored on his first appearance since his midweek loan from Bury to end the Millers' three-game losing run.
The 27-year-old striker charged down Bilel Mohsni's clearance and found the net from just inside the box.
Southend had Elliot Benyon's header disallowed for offside soon after before Rhys Taylor pulled off a double save from two Ryan Hall efforts.
Alex Revell confirmed the win when his 20-yard shot went in off the post.
VIEWS FROM THE DRESSING ROOM
Rotherham United manager Andy Scott tells BBC Radio Sheffield:
"I love the fact that my payers got what they deserved and what they probably deserved from the Dagenham game as well.
"The last three or four weeks in training you've seen it coming together and that was probably the biggest disappointment at Dagenham, that we didn't get what we deserved there.
"With the Torquay game being called off we were itching (to play). The preparation has been difficult with the weather, but that's how you play away from home in difficult positions, against a difficult side.
"You work hard, you become solid as a unit you take your chances and make it difficult for them and really their only chances came from set pieces and long shots."