The magistrate, William Cutler, found Simbarashe Makunike, deputy editor of theFinancial Gazette and the author of the stories, guilty of defamation with actual intent.
"The accused knew very well that he had no evidence ... that it was untrue," Mr Cutler said.
Mr Mugabe has two children with Ms Marafu. But he has denied that he formalised the relationship in 1992 by marrying only months after the death of his Ghanaian wife, Sally.
Makunike said he got the story from Elleck Mashingaidze, director-general of Zimbabwe's Central Intelligence Organisation, to whom he claimed he was related.
Mr Mashingaidze denied this, however, and the magistrate said that the CIO chief gave the impression "of sincerity and truthfulness", while the reporter appeared to be "patently lying".
He added: "You appeared anti-establishment. Your attitude is that denials by anyone in authority must be dismissed. But why should denials be treated with the attitude, 'What else can you expect?' It does not appear fair at all."
He said that to imply that a High Court judge was a liar was "extremely serious", while branding a cabinet minister as untruthful could discourage donor agencies and foreign governments from having any dealings with Zimbabwe.
The magistrate said that the newspaper's editor, Trevor Ncube, had been reckless in publishing the stories, and its publisher, Elias Rusike, was found guilty as a representative of the company. Makunike, Ncube and Rusike had pleaded not guilty to the criminal defamation charges, brought by a High Court Judge, Paddington Garwe, and the Housing Minister, Enos Chikowore, over reports published in April alleging the two had witnessed the secret Mugabe remarriage.
Mr Cutler said that he would pass sentence on 17 August, after considering submissionsfrom the defence and prosecution. The state prosecutor, Bambi Hammond, urged the court to fine the three heavily, because "there was malice on their part". He rejected the defence's pleas for Z$500 (pounds 36) fines or a cautionary sentence against Rusike as paltry penalties, which trivialised the case.
Defamation is usually a civil matter in which the newspaper is sued for damages by the offended party, while criminal defamation is a rarely used charge, implying a much more serious offence.