Derby opened up a three-point lead at the top of the Championship as Steve Howard scored his 12th goal this term.
The visitors ploughed forward in attack and new signing Gary Teale tested Darryl Flahavan with an early effort.
Howard hit the woodwork before he broke the deadlock, heading home Teale's corner on the 33rd minute.
Both sides had chances to score again, Peter Clarke and Mark Gower threatened to equalise while Flahavan made a great save to keep Stephen Pearson at bay.
Southend manager Steve Tilson:
"I'm disappointed because I felt we did enough to take a point from the match.
"Their goal knocked the stuffing out of us but there was a better tempo in the second half. We got in amongst them and controlled the match for long periods.
"It's about how we bounce back, we need to go on a decent run again."
Derby manager Billy Davies on being sent to the stands for swearing:
"I'm disappointed with the handling of the fourth official from the start. I knew it'd be a tough day.
"Sometimes you step outside the technical area but there has been an improvement with fourth officials this season and they are working with us.
"I can't deny using foul and abusive language but I'll do all I can to put in a complaint."
606 DEBATE: Give your thoughts on the match
Southend: Flahavan, Hunt, Clarke, Barrett, Hammell, Campbell-Ryce, McCormack, Maher, Gower (Hooper 76), Eastwood, Bradbury (Harrold 82).
Subs Not Used: Welch, Sodje, Guttridge.
Booked: McCormack.
Derby: Bywater, Edworthy, Moore, Leacock, Camara, Teale (Bisgaard 65), Pearson, Malcolm (Oakley 55), Jones, Fagan (Michael Johnson 83), Howard.
Subs Not Used: Barnes, Lupoli.
Booked: Malcolm, Pearson, Edworthy.
Goals: Howard 33.
Att: 10,745
Ref: I Williamson (Berkshire).