Ituano's sporting director Tiago Cruz has already spent time with Boro, and now an agreement is officially in place.
As part of the deal, Boro have already agreed to take 19-year-old pair Marcos Rhoden and Rafael Peireira on-loan until the end of the season.
Juninho, who sent Carlos Rodrigo Correa and Eduardo Favretto for trials with Boro last summer, will also act as Boro's presence in South America - helping to pick up any talent.
"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," Boro boss Tony Mowbray told the club's website.
"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."
Mowbray stressed that nobody should expect too much from the link-up in the near future.
"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," he said.
"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."
Mowbray, though, admitted that the young Brazilians coming in would get their chance to impress.
"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."
Juninho is considered one of Middlesbrough's finest ever players, and spent three different spells with the club - which included reaching two major finals and also helping them to their Carling Cup win in 2004.