The team's management played the national anthem before players took to the field to prevent Rapinoe from kneeling during the anthem Wednesday night in a gesture of support for Kaepernick, who has refused to stand ahead of at least two preseason games
this year in protest of what he perceived to be institutional racism.
"We decided to play the anthem in our stadium ahead of schedule rather than subject our fans and friends to the disrespect we feel such an act would represent," Spirit said in a statement
"We understand this may be seen as an extraordinary step, but believe it was the best option to avoid taking focus away from the game on such an important night for our franchise."
The statement added that the organization "respect(s) every individual's right to express themselves" but "disagree(s) with her method of hijacking our organization's event to draw attention to what is ultimately a personal -- albeit worthy -- cause.
"To willingly allow anyone to hijack this tradition that means so much to millions of Americans and so many of our own fans for any cause would effectively be just as disrespectful as doing it ourselves."
Rapinoe was "saddened" by the move, according to tweets from Washington Post sports writer Steven Goff.
He tweeted that Rapinoe said it was "incredibly distasteful, four days before one of the worst tragedies in our country, to say I tried to hijack this event."
Rapinoe previously knelt on-field
Sunday during the national anthem before her team's clash with the Chicago Red Stars.
American Soccer Now that the gesture was a "little nod to Kaepernick and everything that he's standing for right now."
Kaepernick has said that he refuses to "show pride in a flag for a country that oppresses black people and people of color."
Alongside Rapinoe, Kaepernick's teammate Eric Reid and Seattle Seahawks cornerback Jeremy Lane have supported the sixth-year quarterback with similar protests.
The San Francisco 49ers quarterback's decision not to stand during pre-game renditions of "The Star-Spangled Banner" has polarized the public.
US President Barack Obama weighed in, saying Kaepernick is "exercising his constitutional right" by not standing for the national anthem.
"I gotta confess that I haven't been thinking about football while I've been over here and I haven't been following this closely," Obama said Monday during a news conference at the conclusion of the G20 summit in China.
"But my understanding, at least, is that he's exercising his constitutional right to make a statement. I think there's a long history of sports figures doing so."
Republican presidential nominee Donald Trump said the athlete "should find a country that works better for him," and told radio host Dori Monson the anthem protest was a "terrible thing."
Kaepernick has said he intends to donate the first $1 million he earns this year to different organizations that help communities, although he did not name specific ones.
"I'm not anti-America," he said. "I love America. I love people. That's why I'm doing this. I want to help make America better."
The Washington Spirit won 2-1, clinching the first home playoff win in the franchise's history.