RSL had already offloaded Fabian Espindola and Jamison Olave to New York Red Bull and now Johnson has joined the pair in finding the exit door at Rio Tinto Stadium.
The Canadian international joined RSL in 2008 and has since made over 100 league appearances for the club.
"Will's arrival in the summer of 2008 was one of the major tipping points in our club's history," said RSL general manager Garth Lagerwey in a club statement. "He was a big part of RSL's foundation, playing a major role in our 2009 MLS Cup championship, our run to the 2010-11 [CONCACAF Champions League] final and our five straight postseason appearances."
Timbers general manager Gavin Wilkinson was thrilled to add the 25-year old attacking midfielder to the Portland roster.
"He will be a key piece moving forward and brings a winning mentality that we feel will be very important to our culture. He is mentally tough and his attitude is infectious. He is also extremely versatile in our system."