The home side took a 1-0 lead into the second leg but that was soon cancelled out when former Reading winger Bobby Convey finished superbly with his trusty left foot in just the 6th minute to make it 1-1 on aggregate.
With 14 minutes remaining, Convey again stepped up with a neat finish when Arturo Alvarez played him into the area to give his side a slight advantage before Red Bulls skipper Juan Pablo Angel headed home a Juan Agudelo cross to make it 2-1 on the night and 2-2 overall.
But MLS Golden Boot winner Chris Wondolowski came up with the winner for the Quakes with nine minutes of regular time remaining. He got on the end of a sweet Convey cross and looped a header over Red Bulls keeper Bouna Coundoul to send San Jose through to the conference final where they will meet the winner of the Colorado Rapids versus Columbus Crew match.
Venue: Red Bull Arena, New Jersey
Crowd: approx. 23,000