The former LPGA Tour major champions eagled the par-5 18th for a one-stroke victory over Sherri Turner and Cindy Figg-Currier (59) on the Granite Links Golf Club course.
The two groups entered Sunday's final round tied at 9-under par. Trailing by one shot, Turner converted a 30-foot eagle putt from off the fringe to pull a shot ahead of Scranton and Johnson.
After Johnson missed a 7-foot eagle putt, Scranton made the 7-footer for the $100,000 first-place check. They finished the two-day tournament at 23 under.
The BJ's Charity Championship is one of four stops on the Legends Tour of the LPGA, and the 30-team field included Nancy Lopez, Rosie Jones, JoAnne Carner and seven members of the Hall of Fame.