Replacement wing Tony Fenner made the difference when he came on in the second spell and kicked four penalties for Southern in atrocious underfoot conditions at Bathgate Park.
It was 6-6 at halftime and when first five-eighth Glenn Dickson kicked two penalties early in the second spell, Pirates led 12-6.
Pirates brought on their heavy cavalry with powerhouse Paul Miller at No 8 and Highlander Mohanri Schwalger in the front row.
Pirates was making inroads into Southern territory with their driving play and had the upper hand. But Fenner's first penalty after 13 minutes rejuvenated Southern and they matched the Pirates forwards and took control in the last 20 minutes.
Southern had attempted to play dry-weather rugby in the first spell but spilled too much ball behind the advantage line. The Magpies restricted their game to 10-man rugby in the second spell and made ground with driving play.
The standout player was No 8 Andrew Stead, who controlled the ball at the back. He made several strong runs and his safe hands did not allow Pirates to feed off Southern mistakes.
Openside flanker TJ Ioane made some dynamic runs with the ball in hand and prop Kees Meeuws used his experience with the pick and go.
Halfback Steve Bruce was the best of the Pirates backs, while Dickson used his powerful boot to punt the ball downfield. Dan Crichton had a lively first half at No 8.
- Southern 18 (Tony Fenner 4 pen, Robbie Smith 2 pen), Pirates 12 (Glenn Dickson 4 pen). Halftime: 6-6. Referee: Ben O'Keefe.