Valeri scored twice in the second half after Rodney Wallace opened the scoring before the break as Portland accounted for San Jose Earthquakes 3-0 at Providence Park.
After coming from behind to win in San Jose on Saturday, the Timbers got the better of the Earthquakes for the second time in less than a week.
Valeri made no mistake from the spot, converting the penalty to the delight of the Portland faithful.
The Argentine midfielder netted his second of the match 21 minutes later, when he tucked away Wallace's initial effort which Earthquakes goalkeeper John Busch failed to deal with.
Meanwhile, Houston Dynamo kept their season alive as Toronto's play-off hopes were dealt a huge blow.
The 10 men of Dynamo were 1-0 winners against Toronto, with Giles Barnes' 35th-minute strike the difference at BMO Field.
Toronto were given a lifeline in the 54th minute, when A.J. Cochran was sent off for fouling Luke Moore inside the penalty area but Jermain Defoe failed to convert the resultant spot-kick.
Dominic Kinnear's men are just a point adrift of a Toronto side that have suffered back-to-back defeats and are three points behind the Crew.
