Owings and Gregorius had been locked in a tight duel for the starting job all spring, and with outfielder Cody Ross starting the season on the 15-day disabled list, it appeared that both Owings and Gregorius would be kept, in addition to backup Cliff Pennington.
But the D-backs decided to carry 13 pitchers rather than 12, leaving them needing to eliminate one position player on the bench, making Gregorius the odd man out.
Gregorius was acquired by the D-backs from the Reds in December 2012, and was tabbed as the club's shortstop of the future.
After a hot start at the plate last year, Gregorius cooled off and Owings tore up Triple-A pitching and then looked good during a September callup, which vaulted him back into the competition.
D-backs GM Kevin Towers said the team felt Owings was ahead of Gregorius at the plate and that the team needed to get every bit of offense it could.
Gregorius has been the subject of trade rumors, but Towers said he is not planning on dealing him.
"We think the world of Didi," Towers said. "I hope he stays a D-back for a long time. I think at some point in time we're going to need Didi Gregorius on the 25-man [roster]."
Owings received the news that he made the team from manager Kirk Gibson just before he drew a walk in the sixth inning Saturday.
"Just a little relief," Owings said. "I've been working really hard this spring and it was a long, tough competition. Just excited to get that news and just go and get ready for the year."