The side from the capital was a step ahead of Southern United for much of the game at Forsyth Barr Stadium.
But a solid defensive display from the home team kept the game close and Southern United had its chances in the second half.
The only goal came in added time at the end of the first half. Southern United had threatened the Team Wellington goal w ith two corners but could not get a breakthrough. Team Wellington swept downfield and forced a corner.
Team Wellington winger Rory McKeown swept in a teasing ball and it found the head of Jack-Henry Sinclair unmarked in the penalty box.
He glanced his header into the left-hand corner, leaving Southern United goalkeeper Liam Little helpless.
It was a cruel blow at the time for Southern United, which had withstood plenty of pressure in the final 20 minutes of the first half.
Southern United tried to get forward in the second half and fashioned a couple of decent chances.
Ben Waide had an opportunity on the left 10 minutes into the second half but sprayed his shot wide. A few minutes later, Adam Hewson fought hard and won a duel with Team Wellington defender Taylor Schrijvers. But his resulting shot went straight at goalkeeper Scott Basalaj.
Southern United coach Terry Boylan was full of praise for his side despite the loss.
"I thought we did well. We had a strategy of having a compact unit and trying to catch them on the counterattack," he said.
"They’re a quality side. They’re in the top two for a reason. I can’t fault our guys. They ran themselves into the ground. Everyone fought hard and played out of their skins. That was the reflection of the scoreline."
He said the goal was just a fact of the player not being picked up.
"They have come down here and played for the result and got the result. But we have to hold our heads up high and remember we have been on a good run. We have lost to a side which could be the premiers as well.
"That was a turnaround from the 6-1 hammering we got in Wellington. The boys are obviously disappointed because we have conceded one goal but that shows how far we have come."
With the loss, the hopes of Southern United finishing in the top four and making the playoffs have taken a significant knock.
Team Wellington always had plenty of men at the back and was lively going forward. Sinclair was classy, while Andy Bevin and Aaron Spain also did good things.
Stephen Last worked hard at the back for Southern United along with Tim O’Farrell, while Cody Brook and Waide ran hard all day. Hewson was all energy, while Garbhan Coughlan was tireless up front.
