Spangenberg's throw home to cut off Alfredo Marte at the plate was deemed late by plate umpire Cory Blaser.
With runners on second and third and no outs, D-backs pitcher Josh Collmenter grounded a ball right at Spangenberg, who threw home to Rene Rivera. But Marte beat the throw on a close play.
San Diego's Bud Black used his manager's challenge, but the call stood after review. Collmenter reached on a fielder's choice and was credited with an RBI as the D-backs took a 2-1 lead in the fifth inning at Petco Park.
The D-backs went on to score three runs in the inning for a 4-1 advantage over the Padres.
Corey Brock is a reporter for MLB.com. Keep track of @FollowThePadres on Twitter. This story was not subject to the approval of Major League Baseball or its clubs.