The 21-year-old was accused of “mocking” the Black Lives Matter movement and “appropriating the resistance” in the commercial, which seems to be inspired by a famous photo of a woman standing up to police at a US protest last year.
But in a statement released on Wednesday evening, Pepsi announced it was removing the advert and apologised for “missing the mark” and putting the supermodel in an awkward position.
In the short video, Miss Jenner, wearing a blonde wig and posing for the cameras, is caught up in the midst of a demonstration when she throws off the wig, grabs a can of Pepsi and hands it to a grim-faced police officer, who accepts it and smiles, to the cheers of the placated crowd.
A spokeswoman for Pepsi said: "Pepsi was trying to project a global message of unity, peace and understanding. Clearly we missed the mark, and we apologise.
"We did not intend to make light of any serious issue. We are removing the content and halting any further roll out. We also apologise for putting Kendall Jenner in this position."
In the YouTube description for the ad, titled ‘Live for Now Moments Anthem,’ Pepsi called it “a short film about the moments when we decide to let go, choose to act, follow our passion and nothing holds us back.”
The soundtrack to the advert is ‘Lion’ by Bob Marley’s grandson Skip.
But once the advert had aired, it sparked an immediate backlash on social media.
“If this Pepsi ad is the choice of a new generation, I'm gonna need that generation to turn in its badge,” wrote comedienne Margaret Cho on Twitter.
Piers Morgan added: “The new @pepsi ad with @KendallJenner is stupefyingly diabolical. Absurd, PC-crazed, virtue-signalling, snowflake claptrap.”
“J. Edgar Hoover takes aim from the grassy knoll. The motorcade approaches. He fires. JFK raises a #Pepsi to his lips, blocks the bullet,” tweeted American comic Paton Oswalt.
Another person posted on Twitter: "Kendall Jenner Pepsi ad summarized: The Revolution Will Be Televised as a Beautiful People Rave With Police as Benevolent Security Guards."
Another joked: "I never knew one can of Pepsi could end police brutality wow thank god for Kendall Jenner", while another simply said: "That Pepsi ad with Kendall Jenner is a real mess ... so much wrong with it."
One person said: "Their new ad campaign is Kendall Jenner showing up at a BLM protest and handing a police officer a Pepsi and suddenly he's happy. Bad taste."
Hitting out at Jenner directly, one person commented: "Tbh i'm really disappointed with the kendall/pepsi advertisement. these various rights movements are NOT some kind of "cool trend"."