Peter Shreeves, the former Spurs and Sheffield Wednesday boss, resigned as the Barnet manager before the game.
He had been in charge for just over a year but said: "I was unhappy that I was not able to give the Bees fans the success they deserve." Coach Martin Allen has taken over the running of the team until the end of the season and was delighted with his team's performance against free-falling Southport.
The first shot on target by the Bees came in the 14th minute when Neil Midgley drilled home a left-footed shot from 15 yards. He was unmarked and the Southport defenders were slow in closing him down.
For the visitors Lee Ashcroft had a left-wing cross deflected for a corner and Dean Howell also attempted a cross and captain for the day Lee Pluck was forced to head the ball for a corner.
John Doolan, recovering from a groin strain, was controlling the midfield and set up Wayne Purser whose header on target forced Steve Dickinson to make another save.
Both Midgley and Frazer Toms went close for Barnet and Keith Rowland and Mark Gower's corners were causing problems for the visitors.
In the second half Doolan limped off the field and was replaced by Lette Baimass. Gower had a run and a left-wing cross and the defenders were unable to clear the ball and Purser was there to head home with a backward flick header.
Five minutes later Southport scored when Kieran Charnock's cross was headed home from ten yards by Paul Wheatcroft.
The same player hit a tremendous shot on goal but luckily for the Bees, Daniel Naisbitt was able to dive and turn the ball away.
In the closing minutes of the game Gower's right-footed free-kick was turned for a corner by Barry Hogan and from Gower's corner Midgley scored his second goal and Barnet's third.