Terms of the agreement were not disclosed.
Johnson, 27, was named to the league's Best XI after helping the Timbers to a first-place finish in the Western Conference regular-season standings and the team's first-ever appearance in the MLS Cup Playoffs last year.
Johnson also helped lead the Timbers to their deepest run in the Lamar Hunt U.S. Open Cup. The team's captain set new career marks in goals (9), assists (5) and minutes played (2,520) during his first season with Portland last season.
The midfielder is a veteran of seven MLS seasons. The two-time MLS All-Star has appeared in 149 career regular-season matches, recording 19 goals and 13 assists.
Prior to joining the Timbers, Johnson spent five seasons with Real Salt Lake, helping the club win an MLS Cup title in 2009.