A Pretoria High Court judge on Wednesday said that there were times when truth prevailed over the rights of privacy.
He then ordered a mother to submit herself and her one-year-old daughter to undergo DNA tests to determine who the child's biological father.
The applicant, a city project manager, brought an application against his former girlfriend, to subject her and her daughter to DNA tests.
The parties are not named to protect the young child.
The man said if the DNA tests established that he was the biological father, then he was entitled to full parental rights and responsibilities.
The applicant and the mother of the child were involved in an intimate relationship from February 2006 until April 2007. The child was born in November last year.
According to her there was no doubt in her mind that the applicant was the father of her child, but he at first denied this.
A few weeks after discovering she was pregnant, she rekindled a former relationship with an old boyfriend, and she subsequently married him.
The woman stated that she was taken aback by the applicant's refusal to acknowledge that he was the father and as her new husband was keen to accept the child, she told the applicant that he was not the father and thus had no responsibilities towards the child.
The applicant, however, made an about-turn and insisted on a DNA test.
The mother, in turn, refused to do this and said it was not in the best interests of the child.
The mother said a DNA test was an invasion of her rights to privacy and dignity.
Judge John Murphy in his judgment said the law on the topic of compulsory blood or DNA testing in paternal disputes was not satisfactory, as there was no legislation which specifically regulated the position in civil cases.
He said judicial pronouncements on "this thorny topic" had not been unanimous in their approach to the issue. In some cases it was found that the court, as upper guardian of children, could authorise a blood test on a minor, while in other cases it was found that the court could not order this. One judge previously said he was not persuaded that the prime objective of the court should always be the ascertainment of the truth.
But Murphy said "truth is a primary value in the administration of justice and should be pursued, if not for its own sake, then at least because it invariably is the best means of doing justice in most controversies".
"Where we come from and who we are, for most people, are questions within the realm of the sacred. To exclude reliable scientific evidence because it involves a relatively minor infringement of privacy more often than not will harm the legitimacy of the administration of justice."
He added that in the light of unmarried biological fathers now having more rights under the Children's Act, it was their right to establish paternity.