Boyer, 27, compiled a 4.41 ERA in 15 relief appearances this year for the Cards, who acquired him in exchange for outfielder Brian Barton in mid-April.
Originally drafted by the Braves in the third round of the 2000 First-Year Player Draft, Boyer has appeared in 144 big league games, all in relief, over parts of five seasons.
Boyer threw five innings of relief for the Cardinals on June 3, and with St. Louis needing to call up a bullpen arm and Boyer being out of Minor League options, the team designated him for assignment.
Boyer is not expected to report to the D-backs until they return home Tuesday. At that time, Arizona will need to clear a spot on the 25-man roster for him.
Steve Gilbert is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.