Eryk Williamson provided assists on both goals for the Timbers, who entered the match with nine players listed on their injury report, including their first- and second-choice goalkeepers.
Logan Ketterer, signed on loan from El Paso of the second-tier USL this week, made five saves, including a 62nd-minute diving stop of Chris Wondolowski's penalty.
It all amounted to Portland's first away win of the season in three attempts.
San Jose was held scoreless for a second consecutive game after scoring 10 goals in their first four matches. This loss came just three days after their previous defeat, a 1-0 loss to undefeated Western Conference leaders Seattle.
But despite outshooting the Timbers 20-18 and holding more than 66 percent of the possession, the Earthquakes found themselves trailing after only five minutes on Saturday night.
Williamson created the opportunity by beating his man in midfield and then slotting a pass diagonally to his right as another defender stepped forward.
Chara reached it inside the penalty area and scooped a chip over the charging JT Marcinkowski that left the goalkeeper little chance.
Marcinkowski made up for it shortly after halftime when he made a flailing denial of Felipe Mora after the Portland striker had snuck behind his marker for an open look on goal.
But Ketterer answered several minutes later after Claudio Bravo was ruled to have handled the ball inside the penalty area.
After coming into the match minutes earlier, Wondolowski stepped up and drilled a low shot toward the right corner, but Ketterer guessed correctly and got down well to push it around the post.
Loria made it 2-0 in the 74th minute, heading Williamson's cross back across goal and beyond a flailing Marcinkowski.