Benitez stunned Goodison Park with a seventh-minute header and Ferguson scored what proved to be the winner five minutes before the break.
Blues substitute Leon Osman reduced the arrears ten minutes after the restart, but City held on to continue the fine form that has made them the Premier League's surprise package.
Birmingham flew out of the traps and their bright start was rewarded in the seventh minute when they went ahead.
Keith Fahey's cross found Ecuadorian Benitez in space in the six-yard box and he clinically planted a header beyond the reach of Tim Howard.
Marouane Fellaini finally had Everton's first effort on goal when he fired over the bar in the 20th minute but City were comfortable.
Steven Pienaar also flashed a shot wide on the half hour but Birmingham were 2-0 up five minutes before the break.
Former Everton favourite James McFadden flicked Sebastian Larsson's cross into the path of Ferguson and he kept his composure to fire home from 12 yards.
But the home side were a different team after the break and after Fellaini had headed over they were back in the game on 55 minutes.
Pienaar found Osman on the edge of the box and the diminutive midfielder stroked his shot past Joe Hart.
Louis Saha blazed another good chance over moments later before his replacement James Vaughan headed over 20 minutes from time.
Everton fans were on their feet 15 minutes from time but it wasn't for a goal as influential midfielder Mikel Arteta made his long-awaited return from injury.
That gave the home crowd a lift but Everton couldn't find an equaliser with Fellaini wasting two half-chances in the final five minutes - on both occasions he failed to test Hart in the Birmingham goal.