When Jones' foot reached back toward the base, first-base umpire Ted Barrett called Lagares safe.
Marlins manager Mike Redmond challenged, and after a one-minute review, the call was overturned. The replay was clear that Jones had the ball in his glove as his foot dragged across the base.
Miami is now 14-for-18 in replay challenges.
Joe Frisaro is a reporter for MLB.com. He writes a blog, called The Fish Pond. Follow him on Twitter @JoeFrisaro. This story was not subject to the approval of Major League Baseball or its clubs.