The ad shows Kendall Jenner leaving a photo shoot to join a heavily policed demonstration.
Kendall Jenner defuses the tension by walking to the police line and handing an officer a can of Pepsi, prompting cheers.
In a statement posted on its website, Pepsi said they did not intend to make light of serious issues.
The much-ridiculed ad was posted to YouTube on April 4 but was no longer accessible there less than 24 hours later.
For nearly two years, there have been protests about the use of force by police against African Americans.
Since last year’s election, there have also been demonstrations against President Donald Trump.
The ad did not specify what the crowds of mainly young, and very good looking, people were marching for. Even their signs only had generic slogans like “conversation” and “voice”.
However, within minutes of the commercial’s launch, observers said it trivialized protests in cities like Baltimore, Maryland, and Ferguson, Missouri, that followed the police killing of black men.
Leading activist in the Black Lives Matter movement DeRay McKesson said: “If I had carried Pepsi, I guess I never would have gotten arrested. Who knew?”
“Pepsi, this ad is trash.”
Pepsi said it was “trying to project a global message of unity, peace and understanding”.
The company’s statement went on: “Clearly we missed the mark, and we apologize.
“We did not intend to make light of any serious issue. We are removing the content and halting any further rollout.”
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