In Rome, Pope Benedict XVI said the act offends the dignity of humankind.
Archbishop Paulos Faraj Rahho was seized by unknown gunmen on Feb. 29, just minutes after he delivered a mass in Mosul, considered the last urban stronghold of al Qaeda in Iraq.
After two weeks of prayers and searching, officials at the archbishop's church received a phone call from the kidnappers on Wednesday, informing them that he had died and where he was buried, Monsignor Shlemon Warduni, the auxiliary bishop of Baghdad, told The Associated Press.
It was not immediately clear if Rahho was killed by the assailants or if he died of an illness. Shortly after his abduction, church officials said they were especially worried because the archbishop was suffering from unnamed infirmities.
A Mosul morgue official, speaking on condition of anonymity for security concerns, said Rahho's body had no bullet holes. The official also said the body was in an early stage of decomposition, suggesting he died a few days ago, and that it was found buried under a thin layer of dirt.
No one has claimed responsibility for the archbishop's killing.
It was the latest violence in what church members call a series of attacks against Iraq's small Christian community.
Last year's International Religious Freedom Report from the U.S. State Department noted that Chaldean Catholics comprise a tiny minority of the Iraqi population, but are the largest group among the less than 1 million Christians in mostly Muslim Iraq.
Since the U.S.-led invasion in 2003, Iraqi Christians have been targeted by Islamic extremists who label them "crusaders" loyal to U.S. troops. Churches, priests and businesses owned by Christians have been attacked by Islamic militants, and many have fled the country.
Benedict deplored the death, calling it an "inhuman act of violence that offends the dignity of the human being and harms the peaceful coexistence of the dear Iraqi people."
In a telegram of condolence sent to the head of the Chaldean Catholic Church in Iraq, Cardinal Emmanuel III Delly, Benedict said he hoped that the "tragic event" would at least help build a peaceful future for the country.
Iraq's Prime Minister Nouri al-Maliki pledged last fall to protect and support the Christian minority. On Thursday, the prime minister said in a statement that "we condemn and denounce this ugly crime and consider it as an aggression that aims to igniting strife among ... the Iraqi people."
In an interview in November with AsiaNews, a Vatican-affiliated missionary news agency, Rahho said the situation in Mosul was not improving and "religious persecution is more noticeable than elsewhere because the city is split along religious lines."
"Everyone is suffering from this war irrespective of religious affiliation, but in Mosul Christians face starker choices," he told the news agency at the time.
The Chaldean church is an Eastern-rite denomination that recognizes the authority of the pope and is aligned with the Roman Catholic Church. The Vatican said at the time of the kidnapping the fact that the gunmen knew Rahho had been celebrating a religious rite indicated the kidnapping was premeditated.