Callum Howe had put the hosts ahead during a strong first-half by Harrogate, but Nathan Clarke levelled before Southwell’s winner for a much-improved Halifax after the restart.
A Halifax win didn’t look on the cards at half-time, but The Shaymen rallied and produced a stirring second-half display to register their first away league win since the opening day of the season, and inflict Harrogate’s first home league defeat in three months.
Harrogate came into the game with a terrific home record - only losing once at home in the league this season and the second highest scorers at home in the division - and you could see why during the opening 45 minutes.
The hosts played some attractive football at times but allied it to a strong work ethic and a real threat from set-pieces.
Howe saw a couple of headers from set-plays go off target early on, while striker Dominic Knowles also had a couple of early sighters.
Michael Woods’ shot from a tight angle was saved by Sam Johnson, but Harrogate were getting closer by the midway point of the first-half as captain Josh Falkingham sent a shot crashing inches wide after a free-kick was cleared to him just outside the box.
Woods came even closer still when he almost capped a flowing, intricate move with a low shot across goal, but Johnson produced an excellent fingertip save.
Woods was at it again moments later with a delightful shot with the outside of his left foot that just dropped past the far post after Harrogate had won the ball on the edge of the Halifax box.
After soaking up an increasing amount of pressure, Southwell then squandered a glorious chance after an incisive counter-attack started by Jordan Preston, who eventually laid the chance on a plate for Southwell, but keeper James Belshaw kept out his shot to the left of the penalty spot.
And that miss looked even worse when Joe Leesley produced his 17th assist of the season when his free-kick was volleyed into the roof of the net from six yards by centre-back Howe for his seventh goal of the campaign, as Harrogate’s pressure finally told.
Liam Kitching nearly added a second from a corner a few minutes later, but he headed it straight at Johnson.
Halifax had come from behind to claim a point in their previous away league fixture at Dagenham, but The Shaymen came into the game as the second-lowest scorers on the road in the division, and needed to offer more of a threat than that solitary Southwell chance.
A clearance by Belshaw went straight to Southwell shortly after the restart, but the keeper was back in goal to catch the Halifax striker’s shot.
It was much better from Halifax after half-time though, as exemplified by Preston’s cute lay-off to Southwell, whose thumping shot was tipped behind by Belshaw.
And from the resulting corner by half-time substitute Ben Tomlinson, Clarke headed in the equaliser at the far post.
The Shaymen had been much more aggressive after the interval, playing with more purpose and energy.
Harrogate had a penalty appeal for handball turned down before Kitching headed narrowly wide from Leesley’s cross.
But Halifax dealt with Harrogate more comfortably once parity was restored, and competed much better
And Southwell completed the gleeful turnaround for the 424 Halifax fans inside Wetherby Road with a drilled shot low across goal.
Southwell could have made it 3-1 in added time but fired wide from near the penalty spot.
Harrogate: Belshaw, Fallowfield, Howe, Burrell, Kitching, Woods (Beck 62), Falkingham, Kerry, Leesley, Muldoon (Emmett 81), Knowles (Williams 84). Subs not used: Thomson, Cracknell.
Scorer: Howe (37)
Shots on target: 5
Shots off target: 11
Halifax: Johnson, Hanson, Clarke, Brown, Sellers, Ferry, Maher, Odelusi (Tomlinson 46), Preston, Kosylo, Southwell. Subs not used: Rowley, Staunton, Edwards, McLeod.
Scorers: Clarke (55), Southwell (88)
Shots on target: 4
Shots off target: 6
Referee: Daniel Middleton
Town man of the match: Matty Brown