Barrett stormed in to convert Mark Gower's 65th minute corner to leave many of the home crowd gasping in disbelief as they had seen it all before.
Barrett said: "This has been a lucky ground for me. When we won here three seasons ago, I scored two and the first one was practically identical to the goal today."
The win keeps the Shrimpers in touch with the leading lights in League One, but this was the first time this season they had beaten a side in the top half of the table.
The Cobblers were left cursing their luck after earning their first penalty since last Boxing Day and only their third in 93 matches.
Perhaps the shock of the occasion was too much as, after referee Roger East had pointed to the spot after a handling offence by Peter Clarke, Andy Kirk's well-struck effort came back off the post.
Northampton enjoyed the better chances from start to finish with Steven Collis making an expert finger-tip save from Bradley Johnson's 20th minute volley from the edge of the box.
He also finger-tipped a thunderbolt from Daniel Jones against the post four minutes before the break.
At the other end, Southend's top-scorer Leon Clarke was always a handful although his finishing was wayward, volleying over the bar from 12 yards in the 24th minute before missing the target again shortly afterwards having broken clear of the last line of defence.
Northampton's biggest home attendance of the season thought they had witnessed a dramatic injury time equaliser, but Alex Russell's screamer skimmed the post.