The defender, 18, has shined in the Montevideo club's youth ranks although he is yet to make his official professional debut, and is currently representing his nation at the South American Youth Championship in Ecuador.
And he will have a new home on his return, as the Catalans announced his incorporation into their Juvenil A side.
"Barcelona and Penarol have come to an agreement for the transfer of Santiago Ignacio Bueno Sciutto," the club confirmed on their official website.
"The player will be a Blaugrana until June 30, 2019, with the option to extend his contract for three more seasons.
"The Uruguayan defender is currently disputing the Under-20 South American Championship with his national team, and when his participation ends he will join the Blaugrana."
While Barcelona declined to disclose the fee for Bueno, Sport reported that Penarol would receive an initial €1 million for his services.
In addition, the Manya could receive up to €5 million if Bueno establishes a regular place in the Barca first team.