Maxime Oliveri bent in a free kick to give Hawke’s Bay United a 3-2 lead, seconds after the side had taken a shot on the advantage from the initial foul.
It proved a defining moment, as neither side scored again and Hawke’s Bay emerged with all three points in Napier.
Southern coach Paul O’Reilly described it as "a little bit of a tough one" but felt his side had chances to come back.
"You’re dealing with fractions of a second, so I’m not going to be too negative towards the referee.
"But certainly it’s one we’d like to see back.
"If the advantage allows them to have a shot at goal and they still get the free kick it’s a double whammy for us.
"It’s disappointing, but we still had plenty of time to get back into it and we played quite well.
"We were the better team in the second half and played some good footbal. We just didn’t do enough, unfortunately."
Southern got off to a good start when a great ball from Garbhan Coughlan allowed Ben Wade to make it 1-0 on the counterattack.
Hawke’s Bay regained control of the game midway through the first half and Sho Goto equalised just on half an hour.
Sam Mason-Smith added a second in the 38th minute, but Southern equalised when Coughlan intercepted a pass and finished well just before halftime.
Olivera put Hawke’s Bay on top, but Southern did not roll over.
Danny Ledwith hit the crossbar twice, while numerous other chances presented themselvesHowever, none were put away.
The result was disappointing, but it was a performance that O’Reilly felt was "still decent".
However, he said it was difficult to win games when you conceded three goals.
The match marked Southern’s sixth away game in its first seven.
That travel hasd been challenging and it is looking forward to returning home to play Canterbury United next week.It has accumulated 10 points despite that, but the team was not satisfied with its return.
"We want more," O’Reilly said.
"I think the days of Southern United being happy with a couple of points on the board and a couple of performances have moved on.
"We’ve definitely improved this year, we’ve got better quality in the squad and we’re playing better football.
"But no, definitely not happy.
"We want more points and we’d like to be thinking we can get to 13 with a positive performance and good result next week.
"Then we need to kick on in the second half of the year."
In the national youth league, Southern claimed its fifth win in six games.
It beat Hawke’s Bay United 4-1 to go to 15 points, one point behind joint-leaders Auckland City and Waitakere United.
Its final game is at home to Canterbury this weekend.
National premiership
The scores
Hawke’s Bay United 3
Sho Goto 31’, Sam Mason-Smith 38’, Maxime Olivera 64’.
Southern United 2
Ben Wade 7’, Garbhan Coughlan 44’Halftime: 2-2
