Barrett headed in corners from skipper Kevin Maher in the 72nd minute and again from substitute Mark Gower at the death to earn the visitors a double over the Cobblers.
It was a dramatic and unexpected turn around which again highlighted the Cobblers' inability to kill off visitors to Sixfields.
Northampton goalkeeper Lee Harper barely had a serious shot to save in the entire 90 minutes, yet twice found himself kicking the ball from the net.
The hosts had the perfect start with a goal in the seventh minute fired home first time by Martin Smith with his right foot after neat approach work by Scott McGleish and Eric Sabin.
The home side created some quality chances in the first half with McGleish firing a rising drive over the bar in the 17th minute while Smith's first time strike on the half hour as he latched on to a Barrett header was saved by the diving Darryl Flahavan.
At the other end, Maher curled a right-foot shot just wide in the 22nd minute and also saw a fierce 30-yarder test Harper.
Northampton again had the better chances to put the game out of Southend's reach in the second half with leading scorer McGleish throwing himself at a Lee Williamson cross but seeing Flahavan tip his header onto the crossbar.
Then a surging run from Sabin brought a diving save from Southend's number one.
But the game turned around with 18 minutes left when Barrett stooped at the back post to convert Maher's corner.
The Cobblers almost immediately restored their lead, with Charlie Hearn's drive hitting McGleish but rebounding just wide with Flahavan wrong-footed.
The finale brought one more chance for the home side with debut substitute Danny Crow firing an angled shot across the goal, but the sting in the tail for the home side was Barrett's last minute header as the home defenders' inability to defend set pieces was again exposed.