Kroc died at her home in the San Diego suburb of Rancho Santa Fe, several months after being diagnosed with glioblastoma, a form of brain cancer, said Dick Starmann, her spokesman.
With an estimated net worth of $1.7 billion, Kroc ranked No. 121 on Forbes magazine's latest list of the nation's wealthiest people.
She inherited the San Diego Padres after her husband died in 1984 and played an active role in running the team until she sold it in 1990 to a group led by Los Angeles television producer Tom Werner.
Her donations created Notre Dame's Joan B. Kroc Institute for International Peace Studies in 1986 and the University of San Diego's Joan B. Kroc Institute for Peace and Justice in 2001. She was also a major benefactor of the Carter Center of Emory University in Atlanta.
Kroc contributed $12 million to establish the Notre Dame center after hearing the Rev. Theodore M. Hesburgh, then president of the university, warn about the arms race at a San Diego talk in 1985, said Scott Appleby, the center's director.
"She walked up to him after the talk and said, 'I'm going to help you,"' said Appleby. "She was a passionate champion of peace and justice and she was single-minded in her dedication to eliminating the threat of nuclear weapons and all forms of deadly violence."
The University of San Diego think tank has worked to broker peace in hot spots including Nepal, Madagascar and the Ivory Coast, said Joyce Neu, executive director, who pegged Kroc's donations to the center at more than $30 million.
Kroc also contributed more than $90 million to the Salvation Army for a 12.5-acre arts and recreation center in east San Diego, said Maj. Cindy Foley, the center's administrator.
"She worried that there were children and families who didn't have an opportunity to discover their talents because of a lack of facilities," Maj. Foley said. "She embodied the word generosity."
Born Aug. 27, 1928 in St. Paul, Minn., Kroc was a musician and music teacher for many years. She married Ray Kroc in 1969 and the couple moved from Chicago to San Diego in 1976, two years after purchasing the Padres and preventing the team's planned move to Washington, D.C.
When Ray Kroc died in 1984 at age 81, his wife succeeded him as the Padres' owner and chairwoman. She admitted knowing nothing about baseball when she took the helm, but that did not stop her from speaking out. The Padres went to the World Series in her first season, losing to the Detroit Tigers.
Kroc was deeply involved in running the team, at one point rehiring Manager Dick Williams after he was fired without her consultation. She sold the team in 1990, not because of the team's poor performance, she said, but because she wanted to spend more time with her family.
"I'm a few years older now, and, unlike Zsa Zsa (Gabor), I'm not ashamed to admit that I'll be 62 next August," she said in a 1989 interview. "I think it's time to prioritize."
Kroc is survived by a daughter, four granddaughters and four great-grandchildren.
By Elliot Spagat