Erick Torres scored his 11th goal of the season to give Chivas victory, which took him alongside Sporting Kansas City's Dom Dwyer in equal second in the goalscoring standings, as the Los Angeles-based team rose to 17 points, one ahead of San Jose.
After a topsy-turvy first half in San Jose, Torres struck seven minutes after the break when a cross from the right skimmed off the heads of two Earthquakes defenders to the Mexican striker and he smashed the ball past Jon Busch at the back post.
Having gone behind, San Jose surged but could not break down Chivas as Wilmer Cabrera's side held on for their second straight 1-0 victory, after accounting for Real Salt Lake on Saturday.
The win took Chivas above the Earthquakes in the West, as San Jose suffered their fourth consecutive defeat in MLS.
In Chicago, the Fire missed the chance for a third win of the season, as they had to come from behind against 10-man Toronto to earn a 1-1 draw.
The visitors had Luke Moore sent off in the 28th minute after he elbowed Chicago midfielder Chris Ritter in the head when challenging for a high ball on the halfway line.
The Fire dominated the rest of the first half but surprisingly went into the break behind after a counter-attack from Toronto saw Jermain Defoe cross from the right wing for Jackson Goncalves to score with a free header.
With the extra space following Moore's red card, Chicago continued to create chances as the rain poured down in the second half with Quincy Amarikwa and Mike Magee both wasting goalscoring opportunities.
The hosts had to wait until the 57th minute when rookie Harry Shipp scored his sixth goal of the season, cutting inside after a short corner to fire a shot past visiting goalkeeper Joseph Bendik.
Chicago had the best chance to win the game but Juan Luis Anangono blasted over the bar with five minutes remaining, as the Fire stayed second bottom in the East.
