The case of Shumail Raj, who was born female but had two operations to remove her breasts and uterus 16 years ago, and Shahzina Tariq has made waves by raising issues of homosexuality and transsexuality that are taboo in the conservative Muslim society.
The couple, who married last year, had approached the Lahore High Court for protection against harassment by Tariq's relatives. However, the judge accused them of lying about the gender of Raj, 31.
Court-appointed doctors examined Raj and decided she was still a woman - something the couple acknowledged later in court. Raj has expressed a desire to go abroad for surgery to become male.
Presiding Judge Kahawaja Mohammed Sharif, announcing their conviction for perjury, said he was issuing a "lenient" sentence, below the seven-year maximum, because they had apologized.
The judge also fined them 10,000 Pakistani rupees (US$165; EUR120) and dropped a charge of committing an act of unnatural lust - which can be punished by life in prison.
Raj and Shahzina Tariq, 26, appeared shocked by the verdict.
Their eyes widened as Sharif announced their punishment, and they briefly clasped each other's arms before police led them away.
Defense attorney Zahid Husain Bilal said the couple would appeal and hoped for an acquittal.
"They were not alerted at any stage of the proceedings that they could be penalized," Bilal said.
Raj, wearing a short-sleeved white shirt and jeans, urged President Gen. Pervez Musharraf to step in.
"We appeal to President Musharraf to intervene," Raj told reporters outside the court. "Musharraf is talking about moderation and enlightenment. We hope he will do something for us."
Asked about the prospect of three years in different jails for women, she said: "No matter, no matter. We love each other."
Tariq, wearing a dark veil, said nothing as the two got into a waiting police van and were driven away.
The court will resume hearings on June 22 on whether to annul the couple's marriage, which Tariq's family says contravenes Islam and Pakistani laws against same-sex unions.
The couple initially said they wed to protect Tariq from being sold into marriage to pay off her uncle's gambling debts. They later admitted they had lied about Raj's gender because they were in love and wanted to live together.
The judge on Monday ordered police to begin a criminal investigation of the surgeons who operated on Raj and report their findings at the June hearing.