Kendall, 21, is said to be devastated after the ad was slammed for undermining the Black Lives Matter movement and Alec, who has known Kendall since she went to school with his daughter Ireland Baldwin, took to Twitter to insist the debacle was not Kendall's fault.
He tweeted: "Don't blame @KendallJenner for that spot. Kendall is still a very young, inexperienced woman in an awful business. Blame her management.
"I remember when my daughter Ireland and Kendall were little kids in school. I think it's unfair to rake these younger ppl over the coals.
"The US is such a sadistically shame-based, blame-centered culture… (sic)."
Kendall has been laying low amid the backlash and is said to have been upset by how it was received.
"The original intent of the commercial was to mirror all the global protests trying to make this world a more equal place for everyone.
But they shouldn't have had a celebrity face tied to it if they wanted to try and send a strong message like this."
Pepsi defended the advert at first, saying it carries an "important message".
In a statement, the company said: "This is a global ad that reflects people from different walks of life coming together in a spirit of harmony, and we think that's an important message to convey."
However, as the controversy failed to fade, Pepsi pulled the advert and released a statement admitting the firm "missed the mark" with the campaign's message.
The statement read: "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 rollout. We also apologise for putting Kendall Jenner in this position."