World Cup winner Juninho, who is now president of the Sao Paulo club, has continued to follow Boro's progress closely since ending his third spell on Teesside in 2004 and has kept in touch with chairman Steve Gibson.
The two men hope the affiliation can benefit all the parties involved over the years to come.
Marcos Rhoden and Rafael Pereira, both 19, will initially be part of Jamie Clapham's squad competing in the Barclays U21 Premier League.
Manager Tony Mowbray said the relationship with Ituano is in its infancy but will give Boro a foothold for the first time in an important football territory.
"Because of the connection with Juninho it's something we think could be a benefit, as we don't have an existing presence in South America and have no scouts there at all," Mowbray said.
"If there are players there with European passports who meet our budget and criteria, why would we not utilise that connection with Juninho's club? Hopefully it will bear fruit over the years."
However, Mowbray was keen to emphasise that fans should not expect too much of the youngsters and that this is only the first steps of a long-term process.
He said: "Juninho's football club aren't going to give us the next Neymar - if they had the next Neymar, he'd be costing someone 20, 30 or 40 million.
"They're not going to let two young players come to us if they were going to help them win their league or win some games.
"They are a couple of young players who are not impacting on their team who they think have the right personality to come here and develop.
"The chairman's talked to them about where we are financially and if they did have the next Neymar, I'm pretty sure he would be going to Manchester United."
But Mowbray is keeping an open mind about the duo and will monitor their progress over the next few months.
"Who knows?" he said. "I'm not going to prejudge them. If they're fantastic for the U21s, well Curtis Main played for the U21s this week and he played for the first team on Saturday. So let's wait and see.
"They won't train with the first team at the moment but it depends on their quality. I'm not closing the door on anyone - as we've seen with Bryn Morris, Jordan Jones, if they do well, we'll bring them in.
"But they're not here as first team players, they're here to join the development squad and see how they get on. It's at the embryonic stages at the moment but let's see how they develop."
Ituano's sporting director, Thiago Cruz, pictured here with Boro chief executive Neil Bausor, has spent time at Rockliffe Park seeing how the club operate and has also visited other club around the world.
Senior Ituano players Carlos Rodrigo Correa and Eduardo Favretto had trials with Boro last summer.
Juninho is fondly remembered on Teesside as one of the club's greatest ever players, appearing in the side that reached two cup finals in 1997 and in the first Boro team to win a major trophy, the 2004 Carling Cup.