The 30-year-old offensive lineman was the Arizona Cardinals' starting right tackle last season, his eighth in the league. He is currently a free agent.
Winston succeeds Domonique Foxworth as NFLPA president. Foxworth was out of the league last season and so could not seek re-election.
NFLPA Executive Director DeMaurice Smith tweeted: "Thank you to (at)Foxworth24 and all the Executive Committee for their leadership. Congratulations to Eric Winston. Lots of great work ahead."
The other candidates for president were New Orleans Saints tight end Ben Watson and former Pittsburgh Steelers safety Ryan Clark, who is a free agent.
Watson and Clark will both serve on the executive committee elected later Wednesday by the union's board of representatives. Clark joined Lorenzo Alexander and Jay Feely of the Cardinals, Zak DeOssie and Mark Herzlich of the Giants, Adam Vinatieri of the Colts, and Scott Wells of the Rams as new members of the executive committee. Watson, Matt Hasselbeck of the Colts, and free agent Brian Waters were re-elected.
Saints quarterback Drew Brees stepped down from the executive committee.
Winston has played for Houston, Kansas City and Arizona since being chosen by the Texans in the third round of the 2006 draft. He played his first six NFL seasons with the Texans, joined the Chiefs in 2012, then moved to the Cardinals last season.
He has served on the union's committees for finance and agent discipline and does community work on behalf of Shriners Hospital for Children.
Winston was elected as a co-alternate union representative by the Texans in 2010.
While in Kansas City, he drew plenty of national attention early in the 2012 season, when he criticized Chiefs fans who cheered when the team's then-quarterback, Matt Cassel, got a concussion during a game.
"It's 100 percent sickening," Winston said that day. "I've never, ever—and I've been in some rough times on some rough teams—I've never been more embarrassed in my life to play football than at that moment right there."
AP NFL website: www.pro32.ap.org