The first half saw few chances created after Southend winger Tommy Black's third minute shot was turned out for a corner by veteran goalkeeper Neil Sullivan .
Neither side was able to make headway against well-drilled defences that soaked up everything that was thrown at them.
But the Blues made the breakthrough on 24 minutes when skipper Kevin Maher picked up a loose ball in midfield to set up Barrett, whose fierce left-foot shot from the edge of the box took a deflection before beating Sullivan.
The lead was shortlived, however, as Doncaster equalised three minutes later following an McCormack foul in the right channel.
Gareth Roberts' resulting free-kick from 25 yards went through a sea of bodies before going in at the far post past a diving Steven Collis.
Rovers took the lead on 36 minutes after Black slipped and Roberts picked up the ball on the left and released Lewis Guy.
Collis parried his shot but the ball bounced off him and into the net.
But Southend got on terms after 50 minutes when Black's centre from the left was flicked on by Matt Harrold for McCormack to head home at the back post for his fourth goal in five games.
Ten minutes later the Shrimpers were back in front after Matt Mills brought down Clarke as he burst into the 18-yard box.
Referee Clive Penton pointed straight to the penalty spot and Clarke nutmegged Sullivan with his spot-kick for his third goal since arriving on loan from Sheffield Wednesday.
Rovers boss Sean O'Driscoll made a triple substitution after 80 minutes and one of them, Sean McDaid, should have grabbed an equaliser on 85 minutes but he shot wide after Mark Wilson's initial attempt was blocked by Barrett.