The single point for the draw moved the Timbers past Seattle into fifth place in the Western Conference.
Both teams came into the match looking to snap winless streaks. San Jose avoided losing its fifth straight match and the Timbers are winless in their last four, all on the road.
San Jose goalkeeper David Bingham made five saves to earn the shutout, including a foot save on a shot by newly signed Timbers designated player Lucas Melano inside the goal box just seconds before Valeri was taken down inside the penalty area to earn the penalty shot.
Adam Larsen Kwarasey needed just three saves in goal for Portland, but the Timbers had to defend 11 corner kicks.