The move by the sports shoe and clothing company ends a relationship that began in 2004 and helped the foundation raise more than $100 million, making the charity's bracelet an international symbol for cancer survivors.
But the relationship soured with revelations of performance-enhancing drug use by Armstrong and members of his U.S. Postal Service team.
Nike said Tuesday it will stop making its Livestrong line of apparel after the 2013 holiday season. Foundation and company officials said Nike will honor the financial terms of its contract until it expires in 2014.
Those terms were not disclosed.
Nike dropped its personal sponsorship of Armstrong last October after U.S. Anti-Doping Agency exposed the team doping program and portrayed Armstrong as its ringleader. And after years of denials, Armstrong admitted earlier this year he used performance-enhancing drugs to win the Tour de France seven times.
Officials at Livestrong, which announced the split on Tuesday, said the foundation remains strong and committed to helping cancer patients worldwide through its survivorship programs.
Armstrong, who started the charity in 1997 as the Lance Armstrong Foundation, was pushed off the board of directors in October and the organization later changed its formal name to Livestrong.
In a statement, Livestrong officials said the foundation is "deeply grateful" to Nike.
"Together, we created new, revolutionary ways of thinking about how non-profits fuel their mission and we're proud of that," the foundation said.
A Nike spokesman did not immediately return a telephone message seeking comment.
Armstrong declined comment, noting he no longer has a relationship with Livestrong or Nike.
Livestrong officials say the charity remains on solid financial ground.
"This news will prompt some to jump to negative conclusions about the foundation's future. We see things quite differently. We expected and planned for changes like this and are therefore in a good position to adjust swiftly and move forward with our patient-focused work," the foundation said.
The foundation said it reduced its budget nearly 11 percent in 2013 to $38.4 million, but said Tuesday that revenue is already 2.5 percent ahead of projections. The foundation also noted that last month, it received a four-star rating from Charity Navigator, which evaluates charities based on financial health, accountability and transparency.