James Kambewa, 26, was pressing for a meeting with Mercy, 4, whom he claimed to be his daughter, which the pop star disputes.
"The extended family members had no knowledge of a father. The village leadership had no knowledge of a father ... the mother was raped and left," the New York Daily News quoted Barbara Charone, Madonna's spokeswoman, as saying.
The Material Girl adopted Mercy last year from a Malawi orphanage after the Supreme Court of Appeal overturned a lower court. She is Madonna's second adopted Malawian child.
Mercy was born in January 2006 to a 14-year-old mother who died days after giving birth. Kambewa, who works as a waiter in Durban, initially vowed to fight the adoption. However, he told the Sunday Times this month that he was happy the star was looking after Mercy.