Gardner, a 26-year-old right-hander, had to be offered back to the Yankees for half of the $50,000 selection cost if he didn't make San Diego's Major League roster.
He struggled in six Cactus League relief appearances for the Padres, posting a 1-0 record and a 7.11 ERA in 6 1/3 innings.
Gardner has spent his entire five-year Minor League career in the Yankees organization. A 13th-round pick in the 2003 First-Year Player Draft, Gardner has a 12-14 record with a 2.88 ERA and 10 saves in 173 professional games, with all but eight of his appearances coming in relief.
Gardner pitched last season at Double-A Trenton, where he was 3-5 with a 2.88 ERA in 44 appearances. In 81 1/3 innings, Gardner allowed 72 hits and 26 earned runs, walking 30 and striking out 66. The Yankees said that Gardner will be assigned to Trenton.
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.