The boys discovered the scrolls, worth more than $250,000, Sunday in the abandoned Tzfat house where they planned to set up a clubhouse, Arutz Sheva reported.
The scrolls had been stolen May 5 from by thieves who broke into Chabad Tzemach Tzedek synagogue.
Upon making the discovery, the boys went straight to the synagogue to share news of their find, said Batya Erdstein, the mother of Ariel Chaim Erdstein, 9, one of the boys.
The boys led rabbis to the scrolls in the abandoned house and police were contacted.
"This is a great miracle," Batya Erdstein said.
On Monday, a procession was held to return the Torah scrolls to the synagogue.
Police were searching for the thieves. There has been speculation they were afraid to move the scrolls from the abandoned house, wanted to wait longer before moving them or that they may have felt remorse and decided against a plan to sell them.