Newly-promoted Doncaster chalked up their second League win with another impressive display against the team that is managed by their former boss Steve Wignall.
Rovers scored a goal in each half and could have had more although Southend battled all the way and finished the stronger side in the last 30 minutes.
Drewe Broughton headed just over the top for the visitors before Doncaster took the lead in the 12th minute when Steve Foster headed home Michael McIndoe's free kick at the far post.
McIndoe hit the post with another free kick five minutes later and Carl Emberson did well to prevent Gregg Blundell adding another for Doncaster soon after.
Southend survived a penalty appeal when Paul Green was sent tumbling by a challenge from Mark Warren in the 27th minute as Doncaster continued to dominate.
Then big striker Leo Fortune-West shrugged off a couple defenders to hit a shot on the turn just over the top in the 38th minute.
Southend's only effort on target in the first half came on the stroke of half time with a tame header from Broughton which was comfortably saved.
Warren was fortunate again when the referee waved play on after he appeared to bring down Blundell early in the second half and the tireless Rovers striker was out of luck again in the 54th minute.
Green put him through and Blundell's long shot beat Emberson but bounced over the crossbar.
Emberson seemed at fault when Rovers made it 2-0 in the 55th minute with Green heading home McIndoe's cross at the far post.
McIndoe had a shot cleared off the line three minutes later before Southend enjoyed a lengthy spell on top as Rovers appeared to run out of steam.
Michael Husbands had a shot cleared off the line and Jim Corbett went close near the end but Rovers finished worthy winners.