The foundation was criticized by some members of Congress and liberal advocacy groups when it decided to stop the funding because of an investigation launched by a conservative Republican into Planned Parenthood's compliance with federal restrictions on funding abortions.
The grant money would be used for breast exams. In a statement Friday, Komen apologized to the public for casting doubt on its mission to save women's lives.
"We have been distressed at the presumption that the changes made to our funding criteria were done for political reasons or to specifically penalize Planned Parenthood. They were not. Our original desire was to fulfill our fiduciary duty to our donors by not funding grant applications made by organizations under investigation," the organization said in a statement.
The foundation said it will make changes to the criteria to clarify that "disqualifying investigations must be criminal and conclusive in nature and not political."
The backlash was swift and harsh, with many accusing the cancer charity of bowing to pressure from anti-abortion groups.
Planned Parenthood supporters responded with millions of dollars in donations in just three days.
Planned Parenthood representatives say it appears the Susan G. Komen for the Cure Foundation caved to political pressure, pulling its annual $680,000 grants after a Florida congressman launched an investigation into the organization at the urging of anti-abortion activists.
"We were really disappointed," said Dinah Stephens, a Planned Parenthood Los Angeles spokeswoman. "We've had a long partnership with the Susan G. Komen Foundation, so we were very disappointed and saddened by that news. We remain committed to serving our patients no matter what."
But then Friday Komen reversed the decision. Founder and Chief Executive Officer Nancy Brinker released a statement Friday apologizing for pulling the funding and said: "Our original desire was to fulfill our fiduciary duty to our donors by not funding grant applications made by organizations under investigation. We will amend the criteria to make clear that disqualifying investigations must be criminal and conclusive in nature and not political. That is what is right and fair."
In the three-day interim, Planned Parenthood was flooded with more than $3 million in contributions, including a $250,000 donation pledge from New York Mayor Michael Bloomberg.
While the donations poured into Planned Parenthood, the criticism of Komen resounded around the country, with many contributors saying they would no longer donate to the iconic breast cancer organization.
Planned Parenthood says that through Komen grants, its health centers provided nearly 170,000 breast exams and more than 6,400 mammogram referrals over the past five years.
In her statement, Brinker also said: "We do not want our mission to be marred or affected by politics -- anyone's politics."
Many believe the original decision was political. Other women say they can see Komen's hesitation to provide funding that may have been perceived as questionable.
Planned Parenthood says every penny of the Komen grant money goes directly to breast health, and that they are cooperating in that investigation.