Vietnam's Communist government earlier rejected a U.S. request for the release of the priest, Thadeus Nguyen Van Ly, saying his arrest was purely a Vietnamese internal affair.
Ly had urged in testimony to a U.S. government committee in February that the U.S. Congress delay ratification of a bilateral trade agreement until Vietnam eases restrictions on religion.
His harsh sentence could speed up U.S. Senate action on a separate Vietnam human rights act that Vietnam's Communist Party has severely criticized.
The act, already passed overwhelmingly by the U.S. House of Representatives, would halt future U.S. non-humanitarian aid unless Vietnam's government improves its human rights record.
Ly was placed under administrative detention, the equivalent of house arrest, after his testimony to the U.S. committee in February. In March, the government also banned him from running his church.
In a one-day trial, a court in central Hue city sentenced him to two years in prison for defying the detention order and 13 years for "undermining the national unity policy of the state."
Vietnam's state-owned television network, VTV, showed a gaunt Ly listening to the verdict with his eyes closed. He was then led out of the courtroom by two police.
The U.S. Embassy had no immediate comment on the sentencing.
Congress has now approved the trade agreement, which was signed into law on Wednesday by President George W. Bush.
Ly's sentencing is the latest in a series of tough actions by Vietnam's government against members of non-approved religious groups.
In September, Ho Tan Anh, a 61-year-old farmer and a leader of the Buddhist Youth Movement in central Vietnam, burned himself to death to protest restrictions on his group.
The Buddhist Youth Movement was founded in the late 1930s by the Unified Buddhist Church of Vietnam, one of a number of independent religious groups now banned by Vietnam's government, which allows only seven recognized religious organizations.
In June, security agents encircled several of the church's temples and placed Thich Quang Do, a prominent priest, under house arrest after he announced plans to escort church patriarch Thich Huyen Quang to doctors for medical treatment.
Quang, 83, who suffers from high blood pressure, arthritis and stomach ulcers, has been under house arrest since 1992.
Vietnam's government says its citizens enjoy religious freedom and insists it holds no prisoners of conscience. But it forbids any independent organizations that might challenge its political and social control.
There have also been persistent reports of harassment of minority groups in Vietnam's Central Highlands who belong to unapproved Protestant ``house churches.''
The Communist Party has orchestrated almost daily rallies against the Vietnam human rights act being considered by the U.S. Congress. It says the U.S. government has no right to interfere in Vietnamese affairs after violating human rights during the Vietnam War.