Ali Adnan and Cristian Dajome scored for the Whitecaps, who also benefitted from a first-half own goal by San Jose’s Brazilian midfielder Judson.
Vancouver led 2-1 at half-time and 3-1 after Dajome scored in the 59th minute, but goals from Chris WondolowskiÂ and Oswaldo Alanis pulled the Quakes level before Salinas’s late strike.
Eight minutes into stoppage time, Salinas brought the ball through the Vancouver defense and beat Whitecaps goalkeeper Maxime Crepeau with a left-footed shot.
The victory lifted San Jose into first place in Group B of Major League Soccer’s World Cup-style tournament that is marking its return from the hiatus caused by the coronavirus pandemic.
San Jose opened the tournament with a goalless draw against reigning MLS Cup champions Seattle.
Vancouver were playing their first match of the tournament, thanks to a schedule reshuffle caused when FC Dallas and Nashville were both forced out of the event because of multiple positive coronavirus tests among players.
Nevertheless, the young Whitecaps side seized the early initiative, taking the lead after seven minutes when Adnan’s shot beat Earthquakes goalkeeper Daniel Vega.
The Whitecaps doubled the lead in the 22nd minute in bizarre fashion.
San Jose surrendered possession following a corner kick and Vancouver forward Yordy Reyna was able to take the ball all the way downfield.
But his cross was deflected into the net by San Jose’s Judson.
Andres Rios pulled a goal back for San Jose in first-half injury time, but Vancouver took a 3-1 lead when David Milinkovic picked off a lazy pass from Vega and found Dajome for the goal.
Wondolowski, Major League Soccer’s all-time scoring leader, started San Jose’s stunning comeback with a header in the 72nd minute.
Alanis made it 3-3 with a header off a corner kick in the 81st before Salinas completed a dramatic win with the clock running out.