The Portugal international has been dropped from the starting XI this season under Luciano Spalletti, sparking rumours of a potential move away.
Manchester United and Paris Saint-Germain have both been linked with the 24-year-old, who joined from Sporting CP in 2016 for around €45 million, but Sabatini says the club have no intention of letting him go.
“As with all those who have to earn their place at the World Cup, Joao has some issues with the lack of playing time," he told Sky Sport.
"We don’t want to lose him, so he and Luciano Spalletti will find common ground and they’ll work out what to do.
"He is our player and we want to keep him."
Just two points off top spot, Inter are expected to invest further in the squad during the next transfer window, as Sabatini confirmed.
“We are in sync with the coach on the intention of making a few adjustments in January," he added.
“We are evaluating the situations for Ramires and Alex Teixeira, it is all yet to be defined.”