Baker scored two tries and added seven points with the boot as the South team claimed a deserved win in the first interisland clash since 1995.
The game was hurriedly arranged as part of the recovery package for the financially stricken Otago Rugby Football Union.
But the players who agreed to be involved showed plenty of commitment, and the crowd (7427) was slightly above expectations.
There were few highlights in the early stages of the second half as both sides made liberal use of a rule allowing them to make 12 changes from the bench.
North closed the halftime gap when Hurricanes centre Richard Buckman popped a deft pass to Blues winger Sherwin Stowers for the try.
But South pushed ahead again when, after a huge overlap on the left, Baker scooted in for his side's fourth try.
Just three minutes later, Baker grabbed his second following a big break by Highlanders team-mate Kade Poki.
There was a popular try to finish the game when Chiefs fullback Robbie Robinson, a good Southland man, scored his second.
North dominated the early stages of the game and scored the opening try after 12 minutes when Blues winger David Raikuna popped a lovely pass to Robinson.
The South struck back with a neat try to Crusaders first five Tom Marshall, and grabbed a second through another Crusader, Adam Whitelock.
The match came to life in the latter stages of the first half following some fisticuffs, with the South capitalising on a shift in momentum by scoring a third try.
It looked doubtful, but the TMO decided Crusaders flanker Matt Todd must have grounded the ball under a heap of bodies.
South 32 (Kurt Baker 2, Tom Marshall, Adam Whitelock, Matt Todd tries; Baker 2 cons, pen), North 24 (Robbie Robinson 2, Sherwin Stowers tries; Lachie Munro 2 cons, pen, Robinson con). HT: South 22-10.
