There was to be no shock result in the top versus bottom clash, with Chris Wondolowski's penalty five minutes before the interval putting the Earthquakes on their way to the three points.
Alan Gordon's 49th-minute strike wrapped up the victory as San Jose extended its margin over second placed Seattle, who could only draw 1-1 at Portland Timbers.
Freddy Montero had put the Sounders on track with a goal in the 57th minute but Portland battled back and Rodney Wallace (78') earned his side a share of the spoils.
FC Dallas left it late to edge out Vancouver Whitecaps 1-0, with Julian De Guzman's last-minute strike settling matters.
Chicago Fire closed the gap to one point on Eastern Conference leader Sporting Kansas City after coming from behind to see off Montreal 3-1.
Impact took a surprise 20th-minute lead through former Italy striker Marco Di Vaio but goals from Sherjill MacDonald (34'), Alexandre Monteiro De Lima (61') and Alvaro Fernandez (80') gave Chicago the spoils.
New York Red Bulls are just a further point behind Fire after Thierry Henry inspired them to a 3-1 win over Columbus Crew.
Henry levelled after Milovan Mirosevic had put Columbus ahead and the former Arsenal and Barcelona star added a third once Dax McCarty had given New York the lead.
Chris Pontius and substitute Lewis Neal were on-target in either half as DC United hit back to claim a 2-1 win over NE Revolution, who had taken the lead through Kelyn Rowe, while rock-bottom Toronto FC and fellow struggler Philadelphia drew 1-1, with Union's Sheanon Williams' 85th-minute strike cancelling out Eric Hassli's goal just before the hour mark.