Stevenage manager Wayne Turner kept his players shut in the dressing room at Haig Avenue after watching them contribute to their fourth defeat in the five most recent Conference fixtures, by having two players sent off after the interval.
The players shown the red card for second bookable offences were Louis Riddle in the 74th minute and Richard Pacquette five minutes from time.
Overall Stevenage made few friends on Merseyside as they combined flashes of skill with far too many heavy tackles, even allowing for the fact that the referee did his best to compensate for the atrocious conditions of continuous rain and a wind which gusted to near gale force at times.
Southport unbeaten on their own ground in the Conference, made most of the early running and took the lead in the 14th minute. Chris Lane laid the ball through to Marc Lloyd-Williams, whose centre from the right was turned into the net by Northern Ireland international Ian Nolan from eight yards.
With the home side keeping up heavy pressure Stevenage had several narrow escapes notably when a header from Barry Jones was cleared off the line by Jude Stirling.
But by then the visitors had equalised five minutes earlier when Dean Howell midway inside his own half, lost the ball to Stuart Fraser who played it out to Richard Howell and his centre saw Pacquette beat Kevin Welsby with a glancing header from close range.
However, Southport regained the lead after 37 minutes with Lane again involved. This time he chipped the ball over the defence and Steve Pickford held off a challenge from Stirling before steering his shot wide of the advancing Mark Westhead.
Despite the conditions and an increasingly treacherous playing surface, Southport played some excellent football and increased their lead to 3-1 in the 73rd minute.
A long kick by Welsby went over the defence and as it bounced substitute Peter Thomson volleyed it home from around the penalty spot.
The dismissal of Riddle ended Stevenage's hopes of a comeback and with Pacquette also sent off five minutes from the end, Southport appeared to be coasting to an easy victory.
However, the visitors cut their deficit to a single goal a minute from the end when a free- kick by Fraser was not cleared and substitute Jack Midson steered a looping header wide of Welsby