Jorge Perlaza was the man for the Timbers, scoring twice before the Fire could answer, in front of a strong crowd of more than 18,000.
The Colombian opened his account for the club in the 29th minute when he rounded his marker and Fire keeper Sean Johnson to slot home into an empty net before Rodney Wallace added a second less than 10 minutes later.
Perlaza then got his second, two minutes into the second half, to make it a 3-0 scoreline essentially giving the visitors no chance.
But the Fire hit back thanks to an Eric Brunner own goal and a Marco Pappa strike to cut the deficit to one goal with nine minutes left.
However, the second own goal of the night came in the 84th minute when Dasan Robinson knocked the ball into the back of his own net after a Jack Jewsbury corner created confusion.
The win allowed Portland to move off the bottom of the Western Conference table whilst Chicago dropped to eighth in the East with their second loss in a row.