Johnson scored in the opening minute on Saturday night and assisted on Alonso's goal in the 66th minute to lift the Seattle Sounders to a 2-1 victory over Colorado and send the Rapids to their sixth straight loss.
"Eddie had a big header for a goal and made a key pass on out other goal," Seattle coach Sigi Schmid said. "Alonso's goal showed why he deserved to be an All-Star."
Seattle (9-5-7) is 2-0-3 in its past five games.
"That win meant more than winning the All-Star game, a game that's more for the fans," Johnson said. "This was all about winning for Seattle Sounders."
Drew Moor scored his third goal of the season in the 3rd minute for Colorado (7-14-1). The Rapids have been outscored 11-3 during their skid.
The Rapids held a lengthy closed-door meeting after the loss.
"We are embarrassed," Colorado coach Oscar Pareja said. "Our fans deserve more than this."
On the tiebreaking goal, Alonso got free of midfielder Wells Thompson, took Johnson's cross, and buried a shot past goalkeeper Matt Pickens for his first goal.
"It all began with great patience by Alex Caskey and then good movement by Eddie," Schmid said. "We finished it off by getting the big goal by Alonso, a player who has done well with previous clubs."
The Sounders have won the teams' first three meetings this year, while allowing just two goals, and have beaten the Rapids six straight times.
"The key was we wanted ball possession and not having to chase them," Schmid said. "We got off to the good start thanks to Eddie's goal, but gave them one right back."
Pickens was denied his 40th career win with the Rapids. He shares the franchise record of 39 wins with Marcus Hahnemann.
The teams got off quickly, each scoring a goal in the first three minutes. Johnson put Seattle on the board in the first minute, putting a header past Pickens off a corner kick from Mauro Rosales.
Moor came right back for the Rapids Brian Mullan worked himself free to the left of Seattle goalkeeper Michael Gspurning. Mullan sent a cross to the opposite wing, and Moor beat Gspurning with a header.
Gspurning stopped a scoring chance by Conor Casey with a sliding two-handed catch in the 15th. Johnson put a low drive on goal and denied a second goal by Pickens in the 24th.
Casey had two chances to tie the game for Colorado. He missed the left post with a header in the 70th. Gspurning made a desperate save to stop an ankle high shot by Casey in the 77th.
"He made a good shot," Gspurning said. "I stayed low to the ground and made a good save."