Payton died March 22 at Johns Hopkins University Hospital in Baltimore after a brief illness, said Lee Daniels, spokesman for the New York-based NAACP fund.
President Barack Obama said in a prepared statement that he and first lady Michelle Obama were saddened to learn that their “dear friend” had died.
He was a “true champion of equality,” Obama said. “The legal community has lost a legend and, while we mourn John's passing, we will never forget his courage and fierce opposition to discrimination in all its forms.”
After graduating from Pomona College in California, Payton went to Harvard Law School and joined the Washington firm of Wilmer Cutler Pickering Hale & Dorr in 1978.
He argued affirmative action cases before the Supreme Court, including Gratz vs. Bollinger in 2003 which involved the admissions policies at the University of Michigan.
The court ruled 6-3 against the university in Gratz but, in a companion case, Grutter vs. Bollinger, the court ruled 5-4 that the law school's race-conscious admissions policy did not amount to a quota system.
Barbara Arnwine, executive director of the Lawyers' Committee for Civil Rights, said Payton's work on Gratz and Grutter showed his long-range strategic thinking.
“He really sat back and said, ‘What is it that the court needs to understand about racial diversity in America? What are the consequences of a non-diverse society?’” Arnwine said
Payton left private practice in the early 1990s to become corporation counsel for the District of Columbia. In 1994, he joined his wife, Gay McDougall, in South Africa, where McDougall was a member of the commission running the country's first democratic elections.
He returned to Wilmer Hale, then became director-counsel and president of the legal defense and educational fund in 2008.
While at the fund in 2010, Payton argued Lewis vs. City of Chicago, in which the Supreme Court unanimously concluded that a group of African-American would-be firefighters had filed a timely charge of race discrimination.
The National Law Journal named Payton to its list of the decade's most influential lawyers in 2010.
Wade Henderson, president and CEO of The Leadership Conference on Civil and Human Rights, said in a statement that Payton “was a warrior for justice and equality.”
“He was arguably a 21st century Thurgood Marshall,” Henderson said. “The highest compliment I could pay him as an advocate is that he could run with the foxes and he could run with the hounds.”
Payton’s survivors include his wife, also a notable civil rights attorney.