Komen's founder and CEO, Nancy Brinker, said in a statement she had accepted Handel's resignation and acknowledged, "we have made mistakes in how we handled recent decisions."
Handel, the foundation's senior vice president for policy, opposes abortion. She was the driving force behind the foundation's decision not to renew parts of its long-standing partnership with Planned Parenthood, the Huffington Post reported earlier this week after reviewing internal e-mails at the foundation. Planned Parenthood operates hundreds of family clinics where abortions are performed.
The Komen foundation later reversed its decision after being faced with a deluge of opposition that included pressure from lawmakers and internal dissent.
"Susan G. Komen for the Cure's mission is the same today as it was the day of its founding: to find a cure and eradicate breast cancer," Brinker said. "We owe no less to our partners, supporters and, above all, the millions of people who have been and continue to be impacted by this life-threatening disease.
"We have made mistakes in how we have handled recent decisions and take full accountability for what has resulted, but we cannot take our eye off the ball when it comes to our mission," she said. "To do this effectively, we must learn from what we've done right, what we've done wrong and achieve our goal for the millions of women who rely on us. The stakes are simply too high and providing hope for a cure must drive our efforts."
Handel had served in her position at Komen since April 2011, Brinker said. "I have known Karen for many years, and we both share a common commitment to our organization's lifelong mission, which must always remain our sole focus. I wish her the best in future endeavors," she said.
A statement from Leola Reis, Planned Parenthood's vice president for external affairs, did not mention Handel, but said, "We are pleased and thankful that the Komen Foundation clarified their grant-making criteria allowing Planned Parenthood affiliates to continue to be eligible for funding of breast cancer screening programs.
"Planned Parenthood staff, board and volunteers have participated in Komen walks. We have always felt welcomed and appreciated as a valued colleague organization in the breast cancer fight."
Handel, a former Georgia secretary of state, was a Republican gubernatorial candidate in Georgia in 2010, losing to current Gov. Nathan Deal in a primary runoff. Former Alaska Gov. Sarah Palin was a Handel supporter.
"Let me be clear, since I am pro-life, I do not support the mission of Planned Parenthood," Handel wrote on her campaign website in 2010.
After Komen's initial decision to cut off some funding, Planned Parenthood said money from the foundation has largely paid for breast exams at local centers. In the past five years, it said, grants from Komen have directly supported 170,000 screenings, making up about 4% of the exams performed at Planned Parenthood clinics nationwide.
The backlash from the decision was immediate. In Washington, 26 Senate Democrats signed a letter calling on Komen to reconsider. New York City Mayor Michael Bloomberg, a longtime Planned Parenthood supporter, pledged $250,000 in matching grants to help make up for the funding loss.
Bloomberg's gift came on top of $400,000 that Planned Parenthood reported raising online from 6,000 donors in the first 24 hours after the initial announcement. By Friday, more than $3 million had been raised, in what Planned Parenthood CEO Barbara Zdravecky said was a "testament to America's compassion and sincerity."
CREDO, which describes itself as the largest corporate donor to Planned Parenthood, said last week that 250,000 of its members had signed a petition urging Komen to reverse its decision. CREDO also had pledged a $200,000 grant to replace the Komen funds for Planned Parenthood.
"The outpouring of support for the work Planned Parenthood does every day on the front lines has been inspiring," Reis said in her statement Tuesday. "And now it's time for us to move forward and continue to provide the prevention services that thousands rely upon every year. One of the best things about this story is that more women known they can rely on Planned Parenthood for cancer screenings."
Several online petitions had called for Handel to be fired, including one from CREDO Action that the organization said Tuesday had some 50,000 signatures.
"Komen may have apologized, but they still need to clean house, starting with the person who drove this atrocious action," the petition said "If Komen wishes to rehabilitate its devastated reputation and gain back trust, Handel needs to be fired."
"The move is clearly connected to attempts by Republicans in Congress to defund Planned Parenthood," the organization said in a statement at the time.
Members began making calls to Komen offices on Tuesday morning before news of Handel's resignation broke, CREDO said.