Doncaster moved to fourth in the table as a result of this well deserved victory, while Southend lost ground in the promotion race.
Skipper Adam Lockwood headed Doncaster in front following an eight minute corner and although Southend equalised ten minutes later, the home side continued to call the shots.
Lockwood's header rocketed into the roof of the net and bounced down and, although it was scrambled away from the goalmouth, the referee ruled that it had clearly crossed the line.
Charlie MacDonald levelled the scores with a diving header that went in off the post in the 18th minute after Nicky Bailey had cut the ball back following a rare defensive error.
The home side pressed on undaunted in the pouring rain with Richie Wellens volleying wide three minutes later before Paul Green hit a fierce shot over the bar in the 26th minute.
Green made no mistake when he restored Rovers' lead on the half hour mark as he lashed home a left foot shot after the ball had fallen to him following another corner from Brian Stock.
In fact all the Doncaster goals resulted from Stock's corners, with the third coming in the 41st minute.
Visiting keeper Steven Collis had produced a superb save to tip a cracking effort from Jason Price round the post.
From the resulting corner, however, Collis punched the ball straight to the feet of Gareth Roberts on the edge of the box and the Rovers left-back hit a swerving left foot volley in off the post.
Southend's attempts to hit back were far from convincing in the second half and, apart from a missed chance by Gary Hooper six minutes from time, they rarely looked like scoring as Doncaster held out comfortably for another valuable win.