Hundreds of fans, wearing Barcelona shirts, as well as a heavy police presence greeted the squad who will train with groups of Israeli and Palestinian children.
The players, who are also visiting Bethlehem, where they were met by Mahmoud Abbas, the Palestinian president, and the Wailing Wall, were working with Palestinian youngsters at Hebron on Saturday night.
On Sunday, they are due to meet Shimon Peres, the Israel president, before coaching more children in Tel Aviv.
"The goals are important but it's also crucial to educate children and try to bring them together," said midfielder Andres Iniesta.
The training sessions are organised by the Peres Centre for Peace as well as the Israeli and Palestinian football federations.
In October 2012, Barcelona caused controversy when former Israeli soldier Gilad Shait, held for five years on the Gaza Strip, was invited to watch the Clasico between Barca and Real Madrid.
It was a decision which sparked calls for a boycott of the Catalan club.
Around 25,000 spectators turned up for the Saturday night training session in Hebron, a crowd which included Mohammad Assaf, the Gaza singer who won the "Arab Idol" talent show earlier this year.
Fans jostled for the opportunity to snap Messi and his teammates on their mobile phones.
After a brief warm-up period, the Barcelona stars played with a group of boys and girls, relaying some of the secrets of their trademark intricate passing game.
Jibril Rajoub, the president of the Palestinian football federation, said he hoped that when Barcelona visited again in the future, it would be in a "an independent Palestinian state alongside Israel".
"Sport is the best way to overcome hate and hostility," said Rajoub who described the visit as an "historic day".
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