Crane, 20, finished with 4-39 as the North fell short on 208 in pursuit of 228-8 in Abu Dhabi.
Durham fast bowler Mark Wood took 2-38 for the North on his return after three ankle operations.
Rain saw the final contest in the inaugural series between players from northern counties and southern counties shortened to 40 overs per side.
The three-match series is designed as a warm-up for county cricket's 50-over competition, the Royal London One-Day Cup, as well as helping players prepare for international cricket.
Eight players earned an automatic place on each team - with North represented by players from northern counties and South from southern counties - through the Professional Cricketers' Association's Most Valued Player ratings formula, while the remaining players were chosen by the England selectors.
The PCA MVP rankings system identifies the match-winners and key influencers of matches throughout the domestic season.
It takes into account conditions, quality of opposition, captaincy and strike-rates as well as runs scored and wickets taken.
South are coached by England assistant Paul Farbrace, while bowling coach Ottis Gibson oversees the North squad.
Hampshire leg-spinner Mason Crane helped the South to a 20-run victory and a 3-0 series win over the North.