Meggs said at a news conference his office reached the decision that prosecutors can't go forward with the case because there was little likelihood of conviction.
The state attorney said there wasn't "sufficient evidence" to take the case to trial and prove there had been a "forceful act."
Winston, 19, was under investigation related to a sexual battery allegation stemming from an incident Dec. 7, 2012. A former classmate of Winston's made the charge against him about a month after the incident, claiming she had been sexually assaulted. Winston's attorney has said sex between his client and the accuser was consensual.
Winston is considered a leading candidate for this year's Heisman Trophy, given to the top collegiate player. Meggs' announcement clearing Winston comes four days before the Heisman Trophy votes are due to be submitted.
Meggs said the timing of his determination about the filing of charges had nothing to do with either the FSU football schedule of the Heisman Trophy voting process.
Winston, a freshman, has completed 218-of-317 passes for 3,490 yards and 35 touchdowns. He's been intercepted eight times. He's rushed for 134 yards and three touchdowns.
He's led the Seminoles to a 12-0 record and the No. 1 ranking in the USA Today coaches' football poll.
Florida State plays No. 20 Duke Saturday in the ACC championship game. If the Seminoles win, they would likely be invited to the Bowl Championship Series title game.