Harbour's win enabled it to claim pole position in pool A and it will play Northland, which was the runner-up in pool C.
Southern will play pool C winner Manawatu.
In the other quarterfinals, Canterbury will play Waikato and Auckland will match up with Tauranga.
The home team was off the pace yesterday. Harbour had a point to prove after it slumped to a 3-1 loss to Auckland B on Tuesday but was quick to seize the initiative, with Petra Dye-Hutchinson scoring from a penalty corner and adding another midway through the opening half.
Tori Taylor smashed in a third before the break and, 15 minutes into the second spell, a dreadful defensive blunder gifted Harbour a fourth. Courtney Winterbottom blasted the goal past Ginny Wilson.
Dayna Holland got one back for Southern thanks to some superb skills from Samara Dalziel. She plucked the ball out of the air and threaded through a beautiful pass which found the classy striker, who added a quality finish.
Southern coach Mark Stafford said his side was not getting too down about the disappointing performance.
"The girls know they did not have their best game today but we're not going to lose too much sleep about it," Stafford said.
"We started to show a bit more in the second half. It was just a few little errors which cost us and they can be rectified."
In the boys' premier tournament, which is being staged in Palmerston North, Southern had a 4-2 loss to Auckland and will play Waikato in a quarterfinal.
