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Shrimpers boss Steve Tilson reckoned his table-topping side needed two more wins to guarantee back-to-back promotions, but instead saw his team become the latest high-flying victims of the resurgent Gills.
Gillingham went into the match on something of a roll, having claimed the scalps of top-six sides Brentford, Huddersfield and Swansea. And they added Southend to that list as the Kent side stretched their run to five wins.
The first real chance of the game fell to 12-goal leading scorer Darren Byfield, but the Gillingham striker's 25-yard shot on 18 minutes was straight at Blues goalkeeper Darryl Flahavan.
The League One leaders eventually tested Gills keeper Jason Brown after 37 minutes when Luke Guttridge's pass found 22-goal top scorer Freddy Eastwood lurking on the right. He tried to lob Brown but the keeper caught the ball.
Southend finally looked to have breached the visitors' defences three minutes later when Guttridge's cross from the right byline was met by Wayne Gray. However, right-back John Wallis was alert to the danger, tackled the Blues striker and put the ball out for a corner.
Gillingham took the lead in the 46th minute when Matthew Jarvis' cross from the left found Black eight yards out. He took a touch then stabbed the ball into the bottom left-hand corner beyond Flahavan's dive for his third goal of the season.
The goal acted as a much-needed wake-up call for Southend, who saw Brown save an overhead kick from Gray and a 25-yarder from captain Kevin Maher.
With the Gills on the back foot, Blues wasted a golden opportunity to equalise on 59 minutes when Guttridge could only fire Gower's left-wing cross wide when he had the goal at his mercy.
Brown then did well to push out Barrett's goal-bound header from a Lee Bradbury right-wing corner for another flag-kick as Southend maintained the pressure.
Despite playing in front of their largest attendance of the season, 11,195, one sensed it was not going to be Southend's day when Maher's goalbound shot deflected off Guttridge but Brown repositioned himself to block the danger.