The Mariners and the right-hander have explored multiyear deals over the past two offseasons, but without success. Hernandez can't become a free agent until after the 2011 season.
Hernandez was 9-11 last season for a Seattle team that lost 101 games; his nine victories were a team high. He also led the Mariners in ERA (3.45) and strikeouts (175). He made at least 30 starts for the third successive season and reached 200 innings for the first time.
"We are pleased to have Felix signed for 2009 and to avoid the arbitration process," new Mariners general manager Jack Zduriencik said in a statement. "It was important to the club to get this done quickly and fairly to avoid any distraction as we prepare for the season."
In 2008, Hernandez became the first Mariners pitcher to hit a home run when he connected for a grand slam off the New York Mets' Johan Santana on June 23 at Shea Stadium. It was the first grand slam by a pitcher in interleague play.
Senior writer Jayson Stark covers Major League Baseball for ESPN.com. Information from The Associated Press was used in this report.