"The minister has carefully considered the appeal for the licence application for Affect05 and has decided to uphold the MDA's position that such performances that promote alternative lifestyles are against the public interest," MDA said.
The couple says their music is about "empowering people to live fulfilled lives, sharing a message of self-acceptance, compassion, love and respect for all people, despite our differences."
"It is the fact that we are gay that is the reason we have been banned by the government from playing at the benefit," said Jason and deMarco in a prepared statement.
Some Singapore officials have been publicly critical of gay men in recent months.
Last November a senior health official blamed a recent surge in HIV infections on the "promiscuous and unsafe lifestyle" of gay men. Since then officials have cracked down on popular gay parties that draw thousands of men from other Asian countries.
Singapore law calls for heavy penalties for consensual gay sex, but enforcement of the law has not been strict.
"We are very concerned about the intolerance against gay people that is expressed and enforced by the government of Singapore, and we are asking people to speak out," Jason said.