Two headers from centre-back Adam Barrett either side of the break ensured last season's League One Champions maintained their unbeaten record at home.
Lee Bradbury added a third late on, before a rare Jonathan Stead strike gave Sunderland a consolation.
Southend made the brighter start and saw winger Mark Gower fire in an 18-yard shot that was saved by Black Cats goalkeeper Ben Alnwick.
The visitors had trouble creating clear-cut chances and were limited to pot-shots from Stead and Rory Delap.
But on 20 minutes Sunderland's Stephen Wright fired a long ball forward which found Daryl Murphy, who cutback for winger Delap to thump a 12-yard shot that Blues goalkeeper Darryl Flahavan dived low to save.
Southend's star striker Freddy Eastwood then saw a penalty appeal waved away by referee Jarnall Singh before Gower released the forward for a one-on-one with Alnwick.
He burst into the 18-yard box on 27 minutes but mis-controlled the ball, allowing the young 'keeper to clear.
Defender Spencer Prior saw his 500th Southend appearance cut short by an ankle injury before Eastwood shot over and Gower's 25-yard effort flew inches wide.
The hosts eventually opened the scoring on the stroke of half-time when skipper Kevin Maher picked Eastwood out and he pumped the ball forward for Barrett to slot home a bullet header from three yards.
The Black Cats came close to equalising seconds after Arnau Riera came on for his debut. Stephen Elliott evaded three tackles but saw his 16-yard shot parried by Flahavan. The ball dropped towards Murphy, who headed over the crossbar on 57 minutes.
Sunderland continued to up the pressure and saw Wright's long distance shot take a deflection to flash just wide of a diving Flahavan.
But the visitors' resurgence was ended on 68 minutes when Steve Hammell's free-kick from the right was nodded back across goal by Peter Clarke at the far post for Barrett to head home his second from close range.
Striker Bradbury made sure of the points by slotting home Gower's cross in the 89th minute, before Stead met a ball over the Southend defence to grab a stoppage-time consolation goal.