The Timbers are tied with Real Salt Lake for best record in MLS with 30 points, the first time in the team's three-year history it has sat atop the league. Portland (7-1-9), also leads the league in goals with 28. It marks a huge turnaround under first-year coach Caleb Porter for a team which finished 8-16-10 last season.
"It's all about the chemistry we have and the workmanlike attitude," Ryan Johnson said.
Colorado (5-7-5) has lost three straight and has just one win in its last six matches.
The Timbers have shutouts in their last three games and five of seven. The last goals Portland allowed at Jeld-Wen Field in MLS play were in a 2-1 loss to Montreal on March 9.
The Rapids started off aggressively Sunday, getting four shots in the first 11 minutes, but it was Portland that got the early goal, Piquionne scoring on a header off a cross from Rodney Wallace in the 12th minute.
Wallace, returning from spending three games with the Costa Rican national team in World Cup qualifiers, had assists on all three goals. He barely missed a goal of his own in the 22nd minute. He then set up Will Johnson's left-footed blast for the second score just before the half.
"You give energy to a team that knows how to play," Colorado coach Oscar Pareja said. ""Going in down 2-0 after the performance we had, it is painful."
Ryan Johnson's goal to seal it in the 84th minute came after Ben Zemanski stole the ball and found Wallace streaking up the sideline. He crossed it in front of the net to Johnson for an easy goal.
"Now, I think it gets even tougher," Will Johnson said. "No more flying under the radar. We're going to get everybody's best now."
Colorado outshot the Timbers 17-6 and kept goalkeeper Donovan Ricketts working throughout the game. Rapids midfielders Atiba Harris and Hendry Thomas returned from serving suspensions, along with Pareja.
Rapids attacking midfielder Martin Rivero announced earlier in the morning that he would be out two weeks as he recovered from a thigh injury.
NOTES: The Timbers have a U.S. Open Cup match against Dallas on Wednesday, while the Rapids remain on the road for a league match with the Montreal Impact on June 29. ... Rapids forward/midfielder Danny Mwanga, who spent his high school years in Portland and played for the Timbers last season, will be sworn in as a U.S. citizen Monday morning. Mwanga came to the United States in 2006 from his native Congo.