The home team had looked good at times in the first half and led 2-1 at the break.
But as soon as United midfielder Conor McDonald was sent from the field early in the second half, after picking up a second yellow card, the home team struggled.
The young visitors gained in confidence and eventually about halfway through the second half found an equaliser.
The ball was crossed from the left and Ben Waine got his head to the ball and put it past Southern United goalkeeper Liam Little.
From there, the Wellington Phoenix hunted for the winner, which would have brought it just its second win of the season, but its finishing was not quite good enough and the United defence stood firm.
United had its chances and midfielder Tony Whitehead hit the post after a nice turn near the end.
Southern United coach Paul O'Reilly admitted his side was not at its best and was lucky to hold on for a draw.
"The red card changed the game, really, but you can't blame the referee, as it was our player who made the challenges. They were two mistimed challenges which deserved a red card," he said.
"I thought it was a poor performance from us today. We just were sloppy in a lot we did. Poor with our skills, poor with the way we hung on to the ball. It just felt like an end of the season game and we were lethargic in a lot that we did."
He said there were some half chances at the end but the side just could not take them.
The game was not helped by a strong wind coming off the nearby estuary, which made it difficult to control the ball.
The first goal after 18 minutes came from McDonald, after Phoenix goalkeeper Zac Jones scuffed his clearance and McDonald pounced to score.
Phoenix replied with a goal from Gianni Stensness but the home side went into the break ahead, thanks to a low header from Azariah Soromon just before halftime.
Best for United were midfielder Whitehead and striker Garbhan Coughlan while Stephan Last was solid at the back.
