In , after four years in the Single-A leagues, Owens was promoted to the Double-A Binghamton Mets where he was outstanding as a closer. He compiled 51 strikeouts while allowing only eight hits in 25 innings pitched before his promotion to the major leagues.
He made his major league debut on July 7, , for the New York Mets. He pitched a perfect ninth inning in a 7-3 Mets loss to the Florida Marlins. On November 20, 2006, the Mets traded Owens, along with Matt Lindstrom to the Florida Marlins for lefties Jason Vargas and Adam Bostick.