Auburn had grabbed a 31-27 lead a minute earlier when Tre Mason ran 37 yards for a score, capping an 8-play, 75-yard drive, but Winston marched the Seminoles right back in closing seconds.
The 2013 Heisman Trophy winner completed a 49-yard pass to Rashad Greene on the drive's second play, bringing the Tigers to the Auburn 23-yard line.
A pass interference call on the Tigers' Chris Davis in the end zone put the ball at the 2-yard line, and on the next play Winston went up high with a pass that Benjamin leapt to catch for the decisive score.
Florida State won its first national championship since 1999 in the final title to be decided under the Bowl Championship Series system.
Winston completed 20-of-35 passes for 237 yards with a pair of scores and ran the ball 11 times for 26 yards.
Greene made nine grabs for 147 yards and Devonta Freeman rushed for 73 yards with a TD on 11 carries.
Mason racked up 195 yards on 34 tries for Auburn, which fell short in its bid for a second national title in four years.
Nick Marshall made good on 14-of-27 throws for 217 yards, two scores and an interception. He added 45 rushing yards on 16 carries.