The decision revealed Friday came two days after state lawmakers stopped short of recommending her husband's removal from office for a top-secret June rendezvous with Maria Belen Chapur.
Jenny Sanford, a former Wall Street executive who helped launch her husband's political career, said Friday their 20-year marriage could not be repaired.
"I am still dedicated to keeping the process that lies ahead peaceful for our family," she said in a brief statement.
A day earlier, the governor told reporters he still hoped they could reconcile. On Friday, he blamed himself for what he called "the moral failure that led us to this tragic point."
"Jenny is a great person, and has been a remarkable wife, mother and first lady," he said in a statement.
Both Sanfords mentioned their four sons, who have lived with their mother at the family's coastal home on Sullivans Island since she moved out of the governor's mansion in August.
"While our family structure may change, I know that we will both work earnestly to be the best mom and dad we can be to four of the finest boys on earth," Mark Sanford said.
Jenny Sanford's divorce complaint on the grounds of adultery did not mention money, property or custody arrangements.
Earlier this week, Jenny Sanford said in a television interview that it was a simple decision to not stand with the governor when he publicly confessed the affair.
"Certainly his actions hurt me, and they caused consequences for me, but they don't in any way take away my own self-esteem," the 47-year-old told ABC's Barbara Walters, who named her one of the most fascinating people of 2009. "They reflect poorly on him."
Mark Sanford, 49, disappeared for almost a week in late June to see Chapur, leaving his staff and his wife in the dark about where he was. His staff told reporters he was hiking the Appalachian Trail. He returned and tearfully confessed the affair at a rambling news conference.
Jenny Sanford said then she was willing to reconcile with the two-term governor, once mentioned as a possible 2012 GOP presidential contender. She weathered the publication of passionate e-mail exchanges between her husband and Chapur, and an Associated Press interview in which he called his mistress his "soul mate" and admitted "crossing the line" with other women.
Jenny Sanford, who is working on a memoir, said she learned about the affair in January when she found a copy of a letter her husband wrote to Chapur. In the months following, he asked several times to visit his mistress. His wife said no.
"It's one thing to forgive adultery; it's another thing to condone it," she told the AP two days after her husband revealed the affair.
