A last-second squandered penalty helped San Jose cling onto three points with FCD making a dramatic effort late.
Marvin Chavez opened the scoring against his old club, placing a skidding volley into the far corner after a Shea Salinas cross found him open at the top of the box.
Alan Gordon doubled the lead seconds before halftime. Sam Cronin lifted a delicate ball to the back post where Gordon won the header.
An hour in, San Jose thought it had iced the match when Brek Shea handled in the area. Chris Wondolowski buried the penalty, but it was called back for encroachment. Kevin Hartman pulled off an impressive double save to keep out the second attempt and its rebound.
That meant when Hernan Pertuz headed home a free kick in the 89th minute, FCD still had hope. It had even more when Simon Dawkins conceded a penalty and Jair Benitez stepped forward in the final minute of stoppage time.
Jair Benitez had never scored in 82 career MLS appearances. He still hasn't. The fullback thwacked his penalty high of the goal and San Jose hung on for the win.
Follow ZAC LEE RIGG on or shoot him an email