The Storm led 1-0 for majority of the game but a costly yellow card to Aimee Heaps reduced the home side to 10 players for the final five minutes.
The visiting side pressed and forced a penalty corner. Goalie Liz Gifford deflected the shot but it fell nicely for former Southern player Kirsty Cole, who smacked it in.
Earlier, the impressive Pip Symes had scored but Southern had been unable to add to its lead, squandering several golden opportunities.
In a tense shoot-out - a relatively new development for hockey - both sides struggled to convert.
Symes scored for Southern and Coles replied for Capital. But the next four players from each side all missed, had shots saved or were timed out (a player gets eight seconds to score).
With the score tied 2-2, the game had to be decided by a sudden-death shoot-out. Symes scored again and so did Cole, but Monique Wilson missed and that paved the way for Tara Hall to score the winner.
She squeezed a shot through, rather than past, Gifford. The ball may have only trickled over the line but it still counted.
While disappointed with the outcome, Brown was pleased with his side's performance.
"The girls played superbly," he said.
"It was a tight game right from the get-go.
"It was end-to-end hockey and both teams played with a very attacking style.
"That is what we aim to do and I felt very proud of the girls with the way they presented themselves.
"Pip played very well up front.
In the midfield, Sofie McLeod and Aimee Heaps both had very strong games and Belinda Smith was a dominant force at the back."
Southern picks up a point from the match with Capital earning two points.
Yesterday's loss was an improvement on Saturday's 4-1 loss to Canterbury in Timaru. The sides were locked 1-1 at halftime but Canterbury scored three second-half goals to seal the win.
"We played some superb hockey in the first half ... but in the second half there were some interesting decisions and we never really recovered."
Eloise Watson broke her hand in the match and Courtney Ross injured her leg.
In other games yesterday, Auckland beat Midlands 2-0, North Harbour thrashed Northland 6-0 and Canterbury dispatched Central 3-0.
On Saturday, Capital beat Central 3-0, Auckland beat Northland 7-1 and Midlands beat North Harbour in a shoot-out.
