A stunning 77th-minute strike from Ricky Ravenhill put Doncaster on the path to ending Southend's record-breaking eight-match winning streak.
Ravenhill's 20-yard thunderbolt broke the deadlock and an opportunist goal from substitute Jonathon Forte two minutes from time ended the League One leader's resistance.
It was a game that could have gone either way but both sides missed chances in a first half played at a scorching pace.
Visiting goalkeeper Darryl Flahavan produced a super save to deny Paul Heffernan, who raced through following a clever turn in the fourth minute.
Mark Bentley placed a powerful header inches wide in the 13th minute and Southend should have gone in front 10 minutes later following good work by Shaun Goater.
It left Mitchell Cole in the clear but his fierce left-foot shot bounced off the startled Jan Budtz in the Rovers goal.
Southend's brand of skilful attacking football was matched all the way by the home side and it was hard to predict which team would be able to seize the initiative.
But the home side finished the half on top and should have gone in front when Heffernan swooped on a slipshod back pass from Lewis Hunt, only to be denied when he tried to push the ball past Flahavan.
Moments later James Coppinger found himself unmarked in the penalty area as he latched onto a pass from Neil Roberts but hit his point-blank shot straight at the keeper.
There was a great chance at the other end in the 33rd minute for Wayne Gray but Budtz raced off his line to block the shot when a goal seemed certain.
The pace inevitably dropped in the second half and it looked to be heading for a stalemate until Ravenhill struck with a goal out of the blue, with a spectacular left-foot shot in the 77th minute.
There was no way back for Southend after that and Forte came on to rattle home a low left-foot shot after latching onto a defence-splitting pass from Paul Green in the 88th minute.
Rovers could have added a third in injury-time but Forte elected to shoot when Neil Roberts was waiting unmarked in the middle with the goal at his mercy.