The freshman phenom becomes the 79th winner of the coveted award which annually goes to the US college gridiron's top player.
Winston, 19 years and 342 days, is the second consecutive first-year freshman player to win the award, following Texas A&M quarterback Johnny Manziel.
"This Heisman isn't just for Jameis Winston, it's for Florida State," Winston said.
The announcement comes just nine days after Winston was cleared of sexual assault allegations stemming from an incident at an apartment in December. Winston's lawyer said his client had consensual sex with the 19-year-old woman.
Winston has thrown for 3,820 yards and 38 touchdowns, both FBS freshman records. He helped unbeaten Florida State climb to number one in the BCS standings for the first time in 14 years.
The 13-0 Seminoles will play number two Auburn for the national title on January 6.
Winston earned 668 first-place votes and 2,205 points, 1,501 more than Alabama quarterback A.J. McCarron, who finished second with 704 points.
Manziel, who finished fifth in voting, threw for 3,537 yards, run for 654 and has totaled 41 touchdowns this season.
Ex-Ohio State running back Archie Griffin remains the lone player ever to win two Heismans, doing it in back-to-back seasons in 1974-75.