After a quiet first half, both sides struggled to produce clear-cut chances after the break. However, San Jose were awarded a penalty in the 63rd minute after Fabinho was adjudged to have handled the ball in the box.
Chris Wondolowski stepped up and converted the spot kick with a low finish. Just ten minutes later, Union were level as substitute Casey rose above everyone else in the box to head home a Raymon Gaddis cross.
Neither side threatened enough in the closing stages of the match but with just four minutes to go, Casey powered another header past San Jose keeper Bingham to seal the win for the visitors.