The husband, Shumail Raj, 31, had sex-change surgery and told a newspaper that a cousin was aware of the condition and agreed to marry because she feared being forced into wedlock with someone else.
The two were arrested last week on the orders of the High Court in the eastern city of Lahore, which said Raj had earlier lied to the court, saying he was a man.
''Neither Islam nor our law allows marriages of the same sex.
This mistake cannot simply be overlooked,'' Lahore High Court judge Khawaja Sharif told the couple.
''Why should a case be not registered against you for committing unnatural offence and telling lie,'' he said.
The judge ordered that Raj be sent to jail in Lahore and the woman, Shezina Tariq, be sent to jail in her home town of Faisalabad, pending their trial.
If convicted of ''unnatural offence'' -- a term used for homosexuality -- they could be sentenced to life in prison.
Tariq said they married because they were in love.
''We're not homosexuals. Ours was a love marriage,'' the 24-year-old woman, clad in a long shawl, told reporters while sitting in a police vehicle after the verdict.
Raj had initially brought their case to the attention of the courts, appealing for protection from harassment by relatives who disapproved of their marriage. Tariq's father had earlier tried to marry her to someone else, the Dawn newspaper reported.
''It was the fear of forced marriage which compelled me to convince Shumail for marriage,'' the paper quoted her as saying.
''I was fully aware of Shumail's physical condition.'' Raj, who has a trimmed beard and looks like a man, had undergone surgery twice in Pakistan and hoped to go abroad for more. Pakistan is a predominantly Muslim nation and sex-change surgery is illegal.
''We love each other,'' Raj told the newspaper. ''I informed her about my medical condition and clearly told her that she could not become a mother if she married me.
''Despite that, Shezina gave her consent owing to fear of forced marriage.'' REUTERS AE SSC1405