Even after this 1-0 win, the Shrimpers are still in grave danger of dropping out of the Football League, yet there was little to choose between the quality of the two sides at Wetherby Road.
Substitute Brendan Kieran hit the crossbar for Harrogate, and when they switched off for a moment defensively, Ashley Nathaniel-George punished them with the only goal of the game.
The chances did not exactly flow in a match that was at times too frantic but still both goalkeepers had the opportunity to make good saves.
Mark Oxley's first was pretty routine, getting to Jack Muldoon's flicked header from a long Dan Jones throw-in after three minutes but the lively Josh McPake playing on the left of a midfield four, would test him more.
McPake's first chance came from a James Belshaw save, the Town keeper denying Nathaniel-George, who had earlier had a shot blocked. Town broke from the corner and although the angle on the right was tight, the midfielder worked Oxley well.
When Josh Falkingham found him with a 25th-minute pass, McPake's run ended with the goalkeeper sticking out his left boot to make an instinctive save. Another run was started by good footwork on the halfway line to get out of a tight spot and ended with a free-kick George Thomson crashed into the wall, and a booking for Jason Demetriou.
Simon Power got to the byline in the 34th minute and stood up a cross Falkingham glanced over and it was a blow to the Sulphurites when the right winger collapsed innocuously running onto a lovely ball down the line from Thomson and hobbled straight into the home dressing room, clutching his right hamstring. To lose McPake too in the second half was especially frustrating.
Passing through the middle of the field was difficult with so many sand-covered bare patches, and Town often opted to go over them, straight into Aaron Martin and Muldoon. Harrogate's inability to get the ball down frustrated Thomson who complained to his team-mates late in the game, “It's like head tennis all the time.”
As the second half went on the cries not only from the field but the dugouts became more frantic, and the football followed suit.
Two Warren Burrell errors ten minutes after the restart gave the visitors encouragement, an underhit backpass forcing Belshaw to come out and make himself big in front of Simeon Akinola, then a clearance ricocheting off the back of Falkingham and into the grateful arms of the goalkeeper. He did at least make an excellent headed clearance from a right-wing cross shortly after.
Despite Belshaw's directions, Town went into the final half-hour getting sloppy in their tracking of men, and they were fortunate Emile Acquah missed the target when given too much space lurking towards the back of the penalty area.
When they failed to pick up a runner less than minutes later, it would cost them.
First, though, they narrowly missed the chance to take the lead themselves.
Power's replacement Kiernan had been making a good impression on the right wing but shot over when picked out by Martin. A minute later Oxley was able to make a comfortable save from McPake after the sting was taken out of his shot.
In the 66th minute a rare bit of good passing football by the hosts ended with Kiernan smacking an outside-of-the-boot shot against the crossbar. Instead, it was Southend who took the lead four minutes later.
No one tacked Alan McCormack's run down the left and while Connor Hall blocked the goalbound shot, he could not stop Nathaniel-George putting the loose ball into the net.
Harrogate continued to push for an equaliser in an increasingly tetchy game which stretched into seven added minutes but a cross Kiernan flashed over from the left was kept away from onrushing substitute Mark Beck, and when his strike partner Muldoon got a glimpse at goal after chesting the ball down, he was unable to put the ball into it.
Harrogate Town: Belshaw; Burrell, Smith, Hall, Jones; Power (Kiernan 39), Thomson, Falkingham, McPake (Francis 73); Martin (Beck 64), Muldoon.
Unused substitutes: Fallowfield, Minter, Williams.
Southend United: Oxley; Demetriou, White (Cordner 46), Clifford, Hobson; Ferguson, Nathaniel-George (Bwomono 90), McCormack (Taylor 76), Olayinka (Holmes 73); Acquah, Akinola.
Unused substitutes: Goodship, Seaden, Mellis.
Referee: L Doughty (Lancashire).
Support The Yorkshire Post and become a subscriber today. Your subscription will help us to continue to bring quality news to the people of Yorkshire. In return, you'll see fewer ads on site, get free access to our app and receive exclusive members-only offers. Click HERE to subscribe.