San Jose's victory ended LAFC's franchise-record seven-game winning streak.
Cowell's decisive goal came in the 77th minute. Tommy Thompson fed him the ball and Cowell was in close proximity to the net and slammed a right-footed shot past LAFC goalkeeper Maxime Crepeau for his second goal of the season.
- MLS on ESPN+: Stream LIVE games, replays (U.S. only)
- Soccer on ESPN+: FC Daily | Futbol Americas
- Don't have ESPN? Get instant access
Benjamin Kikanovic also scored a goal, and Thompson and Cristian Espinoza each had two assists as the Earthquakes (6-11-9, 27 points) halted a six-match winless streak (0-4-2). It is San Jose's first triumph since a 3-2 road win over the Los Angeles Galaxy on July 13.
Kwadwo Opoku scored the goal for Los Angeles FC (18-5-3, 57 points), who still own the best record in the league.
Cristian Arango had a chance to tie the score in the fifth minute of second-half stoppage time after a San Jose turnover in its own end, but his right-footed floater went wide left of the net.
LAFC have dropped four straight matches when playing in San Jose.
LAFC's chances of a comeback were hindered when Ilie Sanchez was called for his second yellow card of the match in the 79th minute to leave his team with just 10 players the rest of the way.
Jeremy Ebobisse had a chance to give the Earthquakes a two-goal in the third minute of second-half stoppage time but Crepeau made the save.
JT Marcinkowski had one save for San Jose. Crepeau had three saves for LAFC.
LAFC had a 12-10 edge in shots but put just one on target. The Earthquakes put five on net.
San Jose grabbed the lead in the 14th minute on Kikanovic's fifth goal of the season.
The Earthquakes made a rush up field and eventually Thompson had the ball and delivered a stellar pass to Kikanovic, who booted the close-range left-footed shot past Crepeau.
LAFC knotted the score in the 54th minute as Kellyn Acosta threaded a pass ahead. The ball went directly to Opoku, who lifted a left-footed shot over Marcinkowski for his seventh goal of the campaign.