"Lord - Protect my family and me. Forgive me my sins, and help me guard against pride and despair. Give me the wisdom to do what is right and just. And make me an instrument of your will," reads the note published in Maariv.
Maariv ran a photograph of the note on its front page Friday. It said the note was removed from the wall by a Jewish seminary student immediately after Obama left.
Obama spokesman Robert Gibbs would neither confirm nor deny the note was Obama's, but the handwriting was similar to another message written by the presidential candidate during his time in Israel this week.
The paper's decision to make the note public brought quick criticism from religious authorities. The rabbi in charge of the Western Wall, Shmuel Rabinovitz, called it an intrusion on Obama's intimate relationship with God.
"The notes placed between the stones of the Western Wall are between a person and his maker. It is forbidden to read them or make any use of them," Rabinovitz told Army Radio.
The newspaper's action "damages the Western Wall and damages the personal, deep part of every one of us that we keep to ourselves," he added.
Many visitors to the 2,000-year-old Western Wall leave notes in its crevices bearing requests and prayers. Obama placed a small note and then bowed his head during a pre-dawn visit Thursday, following a day spent in talks with Israeli and Palestinian leaders.
The Western Wall is the lone remaining outer retaining wall of the second biblical Jewish temple, which was destroyed by the Romans in A.D. 70. Revered as Judaism's holiest site, it stands where the Bible says King Solomon built the first Jewish Temple, which was destroyed by the Babylonians in 586 B.C.
"It's inappropriate that the prayers of a person at the Western Wall should become a subject of public knowledge at all," said Jonathan Rosenblum, a Jerusalem-based analyst of the religious community and director of the Orthodox Am Ehad think tank.
"There is a rabbinic prohibition against reading other people's private communications, and certainly anyone who goes to the wall expects that those communication will be protected," Rosenblum said.
Another Israeli newspaper, Yediot Ahronot, published an article Friday saying it had also obtained the note but decided against publishing it out of respect for Obama's privacy. Nearly all other Israeli media ignored the story.
Thousands of notes and prayers are stuffed into the cracks of the wall. In recent years, the Western Wall Heritage Foundation, which operates the site, has opened a fax hot line and a Web site where people overseas can send their prayers and have them printed out and put in the wall.
The wall is emptied of its notes several times a year. The papers are treated as a prayer book and buried, rather than burned.
While Maariv drew criticism, the removal and publication of the note did not appear violate any laws. Police officials said they were not investigating the incident.
The handwriting appeared to match a message that Obama wrote Wednesday in the guest book at Yad Vashem, Israel's official Holocaust memorial. It was written on stationery from the King David Hotel, where Obama stayed while in Israel.
Obama signed the Yad Vashem message. The note from the Western Wall was unsigned.
At the Western Wall, Obama was greeted by a crowd of curious onlookers and photographers. He donned a white skullcap, listened to a rabbi read a prayer, and inserted a folded white paper between the stones. One hardline Israeli protester shouted, "Obama, Jerusalem is not for sale."
The visit to Israel and the Palestinian territories was part of an international tour meant to shore up Obama's foreign affairs credentials ahead of the November election. Obama's prospective rival, John McCain, visited Israel in March.
