The 30-minute ceremony welcoming the 22-month-old into the Armenian Apostolic Church took place at the Cathedral of St. James in the city's Armenian quarter, the Jerusalem Post reported.
"It was epic. So beautiful," a source close to the family told People.
After the ceremony, Kim, Kanye, Khloe and the kid went to dinner with Jerusalem's mayor, Nir Barkat, E! said. They planned to spend only one night in Israel before moving on to Jordan, the Post said.
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April 14, 8:35 a.m.: A previous version of this story said
They met with the country's prime minister, and their visit was hailed on the government's website.
"Welcoming the guests, the Premier hailed [the] Kardashian family's contribution to the cause of international recognition and condemnation of the Armenian Genocide, highlighting their visit's importance in the run-up to the Genocide Centennial," the website said.
Kim posted pics of the sit-down on Instagram, saying: "It was an honor to meet the Prime Minister of Armenia, Hovik Abrahamyan who expressed how proud they are that we are proud Armenians and we have not forgotten our roots."
The Kardashians are Armenian on their father's side. Attorney Robert Kardashian died in 2003.