However, replays showed that first baseman Brandon Belt caught Crawford's hurried yet accurate throw before Nady's foot hit the bag.
The decision marked Bochy's fourth successful challenge in five attempts.
Padres manager Bud Black took his turn one inning later. With Rene Rivera on third base and one out, San Diego pitcher Tyson Ross hit a chopper to third baseman Pablo Sandoval, whose throw to first was ruled to be in time by Hernandez. But Black challenged the call and a review overturned it.
Ultimately, Sandoval was charged with his fourth error of the year.
It marked the second official challenge for Black and he has won both decisions.
Chris Haft is a reporter for MLB.com. Read his blog, Haft-Baked Ideas, and follow him on Twitter at @sfgiantsbeat. Alex Espinoza is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.