That led to them being stretched for most of the game though they still looked like coming home with a point from their fourth-placed rivals.
But the introduction of Freddy Eastwood made the difference.
The tricky winger came on to slip a ball through the heart of the defence for Mark Bentley to score on 76 minutes. Then Eastwood grabbed an injury-time second as Darlington were caught on the break.
The Quakers created only half chances and with Craig Hignett and Adolfo Gregorio in particular having a bad day the visitors were way short of their fluent best.
They particularly missed the midfield running of injured Adrian Webster though the loss, also to injury, of defender Curtis Fleming was eased by the return of skipper Craig Liddle who had an outstanding game.
Darlington have been hampered by injuries all season but when key players are back a promotion charge is still a strong possibility.
Most of the struggling sides have still to face Darlington and few of them will pose the problems Southend did.
The expected arrival of former Celtic winger Bobby Petta should help perk the side up in time for Saturday's visit to Bury.
Quakers' assistant manager Mark Proctor admitted: "We were well short of our best.
"It was a bad time to have an off-day with Southend just above us in the league, but we had gone five games unbeaten and must now look for another similar run."
