Steven Monjeza, 26, and Tiwonge Chimbalanga, 20, were arrested in December 2009 after celebrating their engagement ahead of a wedding planned for 2010.
They have been in jail ever since and could now face 14 years in prison.
Their arrest had sparked international condemnation and a debate about homosexuality in the country.
Judge Nyakwawa Usiwa-Usiwa convicted both men of engaging in gay sex which he said was "against the order of nature". They are to be sentenced on 20 May.
Same-sex liaisons are frowned upon in Malawi, where homosexual acts are outlawed.
They had denied the charges and their lawyers said their constitutional rights had been violated.
But the Centre for the Development of People (Cedep) and the Centre for Human Rights and Rehabilitation (CHRR) have been urging authorities to relax the country’s stance on homosexuals.
The BBC’s Raphael Tenthani in Blantyre says the government is also coming under pressure from Western donors over the issue.
For a poor country, 40% of whose development budget depends on donors, that is no mean threat, he adds.