The paper's managing editor, Giles Muhame, said he plans to continue publishing photos of gay men in order to "help them live responsible lives".
This month the paper, called Rolling Stone but not linked to the US magazine - published a story featuring a list of what it said were Uganda's 100 "top" homosexuals. Rights activists said the story prompted attacks against at least four gays.
Sexual Minorities Uganda has asked the country's highest court to issue an injunction against publishing the faces of gays in future editions.
"We live in fear," said Julian Onzeima, the group's co-ordinator. "The Rolling Stone paper has led to people turning against us."
Gays in Uganda say they have faced a year of attacks and harassment since an MP introduced a bill in October 2009 that would impose the death penalty for some homosexual acts and life in prison for others.
The bill was drawn up after a visit by leaders of US conservative Christian ministries that promote therapy they say allows gays to become heterosexual.
The bill drew international condemnation and many Christian leaders have denounced it.