Marcos Lopez and Cristian Espinoza also scored goals for the Earthquakes (7-9-9, 30 points), who won for the first time in four September games. Chofis has five goals in his past two games after a hat trick Wednesday against Real Salt Lake.
Sebastian Driussi, Jon Gallagher and Alex Ring each scored goals for Austin FC (5-16-4, 19 points), who saw their losing streak extend to five games. Austin FC has given up 16 goals in the five-game stretch.
The Earthquakes won despite playing without head coach Matias Almeyda, who was suspended because of his actions toward officials following Wednesday's game.
Austin FC took a 1-0 lead in the sixth minute when Driussi scored off the rebound of a Marcinkowski save. San Jose answered 11 minutes later when Marcos Lopez scored on a header from beyond the penalty spot off a corner kick from Carlos Fierro.
Austin FC moved back on top 2-1 in the 35th minute when Gallagher scored from the right side off a pass from Ring, before Ring scored himself 10 minutes later for a 3-1 lead.
The second half was all San Jose as Espinoza scored in the 49th minute when he split the left side of the Austin FC defense and put the ball into the right side of goal.
Chofis went to work starting in the 58th minute when he scored on a penalty kick following a handball on Ring in the penalty area. He added his second goal in the 63rd minute, seeing his initial shot saved by Stuver before converting the rebound for his 10th of the season.
Two minutes after San Jose took the lead, Ring received his second yellow card and was sent off, leaving Austin FC with 10 men and hindering the opportunity to rally.