President Bingu wa Mutharika made the announcement during a press conference with UN Secretary-General Ban Ki-moon in Lilongwe, the capital.
A judge earlier this month convicted and sentenced Tiwonge Chimbalanga and Steven Monjeza on charges of unnatural acts and gross indecency, both colonial-era laws.
The two were arrested in December, a day after they celebrated their engagement.
The case has drawn international condemnation and sparked a debate on human rights in this conservative southern African country.
Homosexuality is illegal in at least 37 countries in Africa, including Malawi.