Missed opportunities early made the Sounders pay for a crucial error late.

Seattle took a first-half lead through Kenny Cooper’s first goal of the season, but a red-card tackle by Djimi Traore changed the course of the game Saturday against the Columbus Crew, allowing the visitors to score twice in the second-half — including a controversial winner in the final seconds — to steal a 2-1 victory at a rainy CenturyLink Field.

The Sounders had been on a 51-game unbeaten streak that dated to the end of 2010 when scoring the game’s first goal, the longest active run in MLS. Crew forward Justin Meram changed that when he collected a short corner kick and curled in a right-footed shot into the far corner of the net to stun a drenched home crowd of 38,469.

There was mass confusion in the buildup to the winner when referee Allen Chapman appeared to stop play to talk to the Sounders but then allowed Columbus to quickly restart before Seattle was ready.

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“If you’re talking to our players, why do you let the ball get played?” Seattle coach Sigi Schmid asked.

The Sounders, who played the final half-hour with 10 men, also were puzzled after falling to 2-2 on the season.

“It was unfortunate how the goal went down with the ref sort of distracting us and us not being 100-percent prepared,” said defender Dylan Remick.

“We have to be smarter on that part,” added goalkeeper Stefan Frei, “but the ref didn’t really help us out there.”

Meram’s goal, in the fourth and final minute of stoppage time, is tied for the latest goal conceded by the Sounders.

Columbus is off to its first 3-0 start in the franchise’s 19-year history.

“Unfortunately we fell asleep on the last play of the game,” said Seattle defender Chad Marshall. “It kills us. It’s frustrating.”

The Sounders, losers of two consecutive at home, fell to 3-8-7 when playing down a man and 5-10-10 in any game they receive a red card.

Trailing 1-0 in the second half, Columbus pulled even on another wild sequence that started in the 58th minute. Forward Dominic Oduro got behind the Sounders’ defense and was tackled from behind by Traore as his shot was blocked by Frei.

Chapman, though, was awarded a penalty kick for the contract from Traore, who was issued a red card for denying an obvious goal-scoring opportunity. Crew star Federico Higuain powerfully finished the PK for his third goal of the year.

Frei’s shutout streak ended at 214 minutes, the longest in MLS this season.

“The penalty kick and the red card became a crucial play,” Schmid said. “At that point, they’re a good possession team and it becomes harder to chase it.”

In the first half, the Sounders had a flurry of chances in up-and-down action and might have been unlucky to only take a 1-0 lead into half.

The goal came in the 22nd minute, when a pass by Obafemi Martins led to a two-on-one breakaway for Seattle. Cooper, who had Lamar Neagle as a passing option to his right, elected to take the shot himself, curling a picture-perfect right-footed effort past goalkeeper Steve Clark.

Neagle, a Federal Way product, had four shots before halftime by himself, including a 21st-minute header and then a 39th-minute shot from the top of the penalty box that resulted in two of Clark’s three first-half saves.

Crucial misses in the end.

“It’s going to be on my mind all night and all day tomorrow,” Neagle said. “If I put a couple of those chances away — I had many — then it’s a completely different story.”

Joshua Mayers: 206-464-3184 or jmayers@seattletimes.com.