Gonzalez had opted out of his deal Saturday, meaning the Yankees had 48 hours to release him or add him to the major league roster.
Gonzalez, 33, joined the Yankees last month on a minor league deal that included $3 million in base salary if he was added to the 40-man roster and a chance to earn $9 million in performance bonuses.
He went 2-1 with a 6.00 ERA in three starts covering 15 innings at Triple-A Scranton/Wilkes-Barre. He had 19 strikeouts and six walks.
With the roster spot created by Gonzalez's departure, the Yankees signed infielder Brad Miller to a minor league contract.
Miller was designated for assignment by the Cleveland Indians last week and criticized the organization for the move.
"Obviously, they don't want the best guys up here," Miller said. "So I'm just trying to take it somewhere else and see what we've got."