The Loons dominated for much of the evening, with Adrian Heath's side testing San Jose goalkeeper Daniel Vega 13 times on the night - three more shots on target than they have registered in a Major League Soccer match in franchise history.
Robin Lod and Jacori Hayes struck first in the early stages of the quarterfinal encounter when they scored within 90 seconds of each other, as Minnesota took a 2-0 lead into the break.
San Jose cut the deficit in half thanks to Magnus Eriksson's penalty, but the lead was short-lived as Luis Amarilla restored Minnesota's two-goal lead minutes later.
Any hope of a comeback was wiped in the 86th when Marlon Hairston scored to put a bow on Minnesota's decisive victory.
The Loons will have five days to rest before they take on Orlando City in the semifinals on Aug. 6 at the ESPN Wide World of Sports Complex.
Minnesota cruises past San Jose to reach MLS semifinals