The throw came back to first, where pitcher Cody Allen was covering, and first-base umpire Brian Knight ruled Roberts out to complete an inning-ending double play.
Yankees manager Joe Girardi challenged, and after a review of two minutes and 24 seconds, the call was overturned and ruled a fielder's choice.
But the play became moot after Allen struck out Ichiro Suzuki to end the inning, leaving Derek Jeter and Roberts on base.
Girardi and the Yankees have made 17 challenges this season, with 13 calls overturned. Two calls were confirmed and one was ruled to stand.
Bryan Hoch is a reporter for MLB.com. Follow him on Twitter @bryanhoch and read his MLBlog, Bombers Beat. This story was not subject to the approval of Major League Baseball or its clubs.